Round-up
Payroll software for S corps (2026): the Owner-Employee Test
Payroll software for an S corp has one job most tools skip: paying a working owner as a W-2 employee and reporting the 2% shareholder health premium in the right W-2 boxes. Of twelve tools read on 30 August 2026, six publish a payroll-only price for one employee, $36 to $55 a month, and six document that item.
Payroll software for an S corp is mostly ordinary payroll software with one extra job: paying the owner as a W-2 employee, on a fixed salary, and reporting the owner’s health premium the way the IRS wants it on the W-2. We read twelve payroll tools on 30 August 2026, from the five that rank for this search to the two big quote-only vendors and one back-office bundle, and asked each the same five questions. Six publish a payroll-only price for one employee, from $36 to $55 a month; a seventh, QuickBooks, prices payroll only inside an accounting bundle. Six document a pay item for the 2% shareholder health premium in their help centres, and one of those six names the W-2 boxes it lands in; ADP names them too, in a support PDF rather than a product article.
The first page of results is not going to tell you this. On 29 August 2026 it was four payroll vendors, a thread on r/smallbusiness titled “Payroll for 1 - S Corp - do I need software?”, a YouTube video, and two “best of” lists, one of them published by a payroll company. No independent tester, and no page that prices the thing a one-person S corp actually buys: one employee, twelve months, forms included.
Be clear about what this page is and is not. We run our own payroll on Gusto and rate it 8/10 in our review; we have not run an S corp owner’s payroll, or a 2% shareholder health item, through Gusto or any other tool here. Every price and feature below is quoted from the vendors’ own pages and help centres or, where we say so, from their dated archive copies, support PDFs and community answers, and every tax rule from an IRS page with its revision date, because a page about payroll for a corporation you own is not a place for paraphrase. There are no scores except Gusto’s, no screenshots of an S corp payroll we ran, and no affiliate links on this page. Three vendor sites, OnPay, Patriot and Intuit, would not serve our network that day; their figures come from their help centres and from dated archive copies of their pricing pages, and we say which each time. Nothing here is tax advice: the IRS quotes say what is reportable and where, never how much your salary should be.
The Owner-Employee Test: five questions for any payroll tool
The IRS is unusually plain about the first premise. Its page on S corporation employees, shareholders and corporate officers, reviewed 4 July 2026, says the definition of an employee for FICA, FUTA and withholding “includes corporate officers”, that “the fact that an officer is also a shareholder does not change this requirement”, and that courts “have consistently held S corporation officers/shareholders who provide more than minor services to their corporation and receive, or are entitled to receive, compensation are subject to federal employment taxes”. Its compensation page, reviewed 3 March 2026, sets the order: reasonable compensation “before non-wage distributions may be made”. So an owner who works in the business is an employee (the same page excepts an officer “who performs no services or only minor services and who neither receives nor is entitled to receive any pay”), the salary comes before distributions, and the tool has to handle both the salary and what rides on it. Ask these five things, in this order, and stop where the answer is no.
| Question | What the IRS pages say | What to look for on the vendor’s pages |
|---|---|---|
| 1. Will it pay the owner as a W-2 employee on a fixed schedule? | Payments to an officer “must be treated as wages to the extent the amounts are reasonable compensation” (Form 1120-S instructions, reviewed 30 April 2026) | A plan that names owner-only payroll, and an auto-run for a salaried employee so the schedule holds |
| 2. Does it file everything, and in how many states? | Form 941 quarterly by default; Form 944 annually only “if the IRS notified you in writing” and your annual liability is $1,000 or less; Form 940 at 6.0% on the first $7,000 of wages, less a credit of up to 5.4% for state unemployment tax paid; W-2 and W-3 | Federal and state returns included in the base price, with the number of states and the fee for a second one written down |
| 3. Does it document the 2% shareholder health item? | Premiums for a more-than-2% shareholder are “reportable as wages on the shareholder-employee’s Form W-2”, included in box 1 but not boxes 3 and 5 when paid under a plan for employees, with an information item in box 14 (box 14a on 2026 forms) | A help-centre article with a named pay item or benefit, ideally naming the boxes |
| 4. What does one employee cost for a year? | Nothing to say | Base plus one seat, times twelve, plus the fees that only show at year end |
| 5. What will it not do? | ”Reasonable compensation” has nine listed factors and no formula | Owner’s draws, a second state, contractors, and any promise about the salary amount |
Two things the test leaves alone on purpose. It does not score the salary calculators several vendors advertise, because the IRS lists factors and no method, and it does not touch what your state does with an officer’s wages: the Form 940 instructions warn that “in certain states, wages paid to corporate officers” are excluded from state unemployment tax, which can raise your federal rate to the full 6.0%, and that is a question for your state’s page, not a payroll vendor’s. If a public-works contract is in your future, the certified payroll tools we read are a separate purchase from everything below. And if the entity paying you is a 501(c)(3) rather than an S corp, the hard question moves from the owner’s W-2 to the grant the salary is charged against: payroll software read against restricted funds is the shortlist for that case.
At a glance: twelve tools against the test, read 30 August 2026
Prices are list prices for one employee in one state, before promotions. “Documented” means we found a help-centre article or product page that names the item; “not stated” means we did not find it on the pages we read that day, not that the feature is absent. The last column matters more here than anywhere else on this site: when the company is one person, a filing calendar that runs without a click is the clearest case of HR automation removing work rather than relocating it.
| Tool | One employee, per month and per year | Federal and state filing | 2% shareholder health item | Owner-only plan or page | Runs payroll automatically |
|---|---|---|---|---|---|
| Gusto Solo or Simple | $55 · $660 | Yes; Simple covers one state, Plus ($80 + $12) covers several | Documented; boxes not named | Yes, Solo plan | Yes, AutoPilot |
| Patriot Full Service | $42 · $504 (archive copies) | Yes, 50 states; $12/mo per extra state | Documented; box 1, box 14 “SEHI”, box 16 named | Not stated | Yes |
| OnPay | $55 · $660; first month free | Yes, all 50 states, no multi-state fee | Documented (updated 10 December 2025); boxes not named | Yes, S corp page; single-member price unpublished | Not stated |
| SurePayroll Full Service | $36 · $432, plus $50 + $5 per form at year end | Yes; one state, $9.99/mo for more | Documented (December 2023); boxes not named | Yes, S corp page; limit of five active officers (December 2023) | Yes |
| Square Payroll | $41 · $492 | Yes, all 50 states and DC; 941 or 944, 940, W-2/W-3 | Partial: a 2023 community answer from Square staff, entered once a year | Not stated | Yes |
| Wave Payroll | $46 · $552; 30-day trial | Yes, all 50 states; 1099-NEC generated, not filed | Documented as a named benefit (updated 15 June 2026); boxes not named | Not stated | Not stated |
| QuickBooks Workforce | $95 · $1,140 (payroll + accounting bundle, 26 August reading) | Yes; some local taxes on higher tiers | Documented; a solo owner with no employee plan is sent to Desktop | Page, not a plan | Yes, salaried on direct deposit |
| ADP RUN | Quote-only; article says $127.95 per quarter officer-only | ”Federal, state and local” | Documented in a support PDF: box 1, box 14 “S-CORP” | Yes, “Payroll for one employee” page | Yes, RUN & DONE |
| Paychex Flex | Quote-only | Claimed | Partial: named on a year-end checklist only | Yes, page without a price | Not stated |
| Collective S Corp Tier | $349 · $4,188, or $3,560 billed yearly | Yes, through Gusto | Documented, entered by Collective’s team in Gusto | Yes, the whole product | No: “Run Payroll - W/O Autopilot” |
| Deel Payroll | $29 · $348 if it takes one employee; minimum not stated | Yes, all 50 states | Not found | Not stated; every card ends in “Book a demo” | Not stated |
| Rippling | Quote-only | Not stated | Not found | Not stated | Not stated |
Read column three before column two. The cheap end of the price column is real, but a $36 tool that makes you file a ticket to get the health premium onto the W-2 in December costs you an afternoon and a nervous week. Our dated pricing index tracks the general payroll tools as they move; SurePayroll and Collective are not on it yet.
Do you need software at all? The Reddit question, answered from the forms
The thread that outranks most of the vendors asks whether a one-person S corp needs payroll software. The requirement is the filings and the deposits behind them; the software is one way to get them done, and the cheapest full-service tools here start at $36 a month. For one salaried owner in one state the calendar is Form 941 four times a year (due the last day of the month after each quarter, per the March 2026 instructions), Form 940 once (due 2 February 2026 for 2025, or 10 February if every deposit was on time), a W-2 and W-3 in January, your state’s withholding and unemployment returns, and the deposits behind all of them. Form 944 replaces the four 941s only for employers whose annual liability is $1,000 or less, and only if the IRS has told you in writing to file it; the instructions say “if the IRS didn’t notify you to file Form 944, don’t file Form 944”.
That is the list a $36-to-$55 tool takes off your desk. No IRS page we read requires a payroll provider; what the pages require is the withholding, the deposits and the returns, and the Paying yourself page names what follows when they are missed: liability for the taxes you failed to withhold, “including yourself if you are a corporate officer”, and possibly a trust fund recovery penalty. If the budget really is zero, the free payroll tools we compared are built around that trade: no filing done for you, or filing behind a paywall. For everyone else, the week-one questions in our payroll buying guide still apply, and a second state is the one that most often moves an S corp owner off the cheapest plan.
Gusto: the only owner-only plan with a published price
Gusto Solo is the one plan in this round-up built for a company with no W-2 employee except the owner. The page, read 30 August 2026, prices it at “$49/mo base + $6/mo per payroll recipient”, rounds that to “most owners pay $55/month”, and lists “S-corp payroll with automated tax withholdings & quarterly filings”, “quarterly 941 filing, all 50 states”, a guided Form 2553 election, W-2 and 1099 generation and a reasonable salary calculator. Gusto’s help centre describes Solo as “best for owner-only businesses with no W-2 employees besides the owner”, including “owners who are an S corp or thinking about it”, and confirms month-to-month billing with no contract. The regular Simple plan is the same $49 plus $6, covers one state, and adds AutoPilot payroll; Plus, at $80 plus $12, is where multi-state payroll starts.
On the 2% shareholder item, Gusto has a dedicated article, “Update 2% shareholder status for S-Corp employees in Gusto”: the company must be set up as a C corporation or LLC taxed as an S corp, the owner is marked with a “2% Shareholder” dropdown, and Gusto warns that the status “affects how we tax their health insurance premiums”. It does not name the W-2 boxes, and it carries no date. The limit that matters is in the same article: “we do not support 2% shareholder owners who need both a taxable salary and a non-taxed owner’s draw”; the draws go outside Gusto. We run our own payroll on Gusto, which is where the 8/10 comes from, and the AutoPilot we tested is the one we scored in our automation round-up; we have not run a shareholder item through it, so that part is Gusto’s documentation, not our test. If Gusto is the plan and the price is the problem, the alternatives we priced start from published grids.
Patriot: the only help centre that names the W-2 boxes
Patriot’s site blocked our network on 30 August 2026, so what follows is read from archive copies of its pages dated 29 July, 2 August and 17 May 2026, and should be confirmed on patriotsoftware.com before you buy. Full Service Payroll is listed at $37 a month plus $5 per worker paid, with federal, state and local filings and deposits, year-end filings at no extra fee, free direct deposit, unlimited payrolls and auto payroll; Basic Payroll at $17 plus $4 files nothing and fails question 2. Patriot files “in all 50 states with our Full Service Payroll”, with “a $12 fee for each additional state”, so a two-state owner pays $54 a month, not $42.
Its article “How To Add S Corp Health Insurance Premiums To Payroll” is the one document in this round-up that reads like the IRS page. You create a company-level contribution, choose the taxability “S Corp Health Insurance”, and the article states what happens next: “the ‘W-2 Box’ field will prefill to ‘Box 14 - Other’ with a label of ‘SEHI’”, and the year-to-date amount “will be added to the total in Box 1 for federal taxable wages, Box 16 for state taxable wages (when applicable), and Box 14”. It also says Patriot “will NOT be collecting the income taxes associated with the S Corp Health Insurance Contribution”, which is a withholding conversation to have with your accountant before December, not after. Note the 2026 W-2 instructions have split box 14 into 14a and 14b; the vendor articles, Patriot’s included, still say box 14. No S corp landing page and no owner-only plan; the archive copy also showed a promotion, 30 days free and 50% off for six months, marked as ending 31 August 2026.
OnPay: every state included, and a single-member price it will not print
OnPay’s site returned errors from our network on 30 August 2026; its help centre did not. The help article “OnPay Pricing”, updated 1 May 2025, gives “$49 base fee plus $6 per person”, with “tax filings and payments in all 50 states” in the base fee and a promise that “we never charge for extras like tax filings and payments in multiple states, off-cycle runs, or run cancellations”. The per-person fee applies once a month to anyone paid at least once in the billing period, year-end forms are free to self-print or $10 each by mail, and the article notes that SaaS subscriptions carry sales tax in many states. An archive copy of the pricing page dated 15 July 2026 shows the same $49 plus $6 per worker, “get one month free”, state new-hire reporting included, and an HR add-on at $15 plus $2 per worker.
OnPay’s S corp page, read from an archive copy dated 16 April 2026, is written for one person: “S Corp payroll for solopreneurs”, filings “whether you run payroll monthly, quarterly, or annually”, blank filings included, and a line the other vendors do not have: “we even offer special pricing for single-member organizations, if you’re only paying yourself a couple of times a year. Talk to us to learn more.” The price is not published, so it does not appear in our table. The health item is documented in “Adding 2% shareholder benefits to W-2s”, updated 10 December 2025, with pay types for shareholder insurance, HSA and auto, a rule that the taxable amount “must be processed as a pay run on or before December 31 of the same tax year”, and a warning that adding it after the new year takes a support ticket. Boxes are not named. Whether payroll can run itself is not stated on the pages we could read.
SurePayroll: the lowest monthly price, with two fees to add back
SurePayroll’s Full Service plan is $29 a month plus $7 per employee on 30 August 2026, so $36 for one owner, with taxes “filed & deposited”, automatic scheduling, unlimited runs and two-day direct deposit. Two lines lower on the same page change the year: “first state included, multi-state payroll for $9.99/month”, and “year-end W-2 and 1099-NEC forms are billed annually - not monthly - at a $50 base fee plus $5 per form”. One owner, one state, one W-2 is $432 plus $55, or $487 a year, which is still the lowest full-service figure in this round-up. The No Tax Filing plan at $20 plus $4 leaves every deposit and return to you and fails question 2.
The S corp page is the plainest on the market about the premise, “even if you’re the only employee, you must run on a consistent schedule”, and “salary must come first”. Two help-centre articles carry the S corp specifics, both dated December 2023: one sets up an “S-Corp 2% Owner” earning entered under other compensation on the payroll screen, boxes not named; the other explains that SurePayroll limits the S corp product to “five active employees (officers)” because, it says, most S corporations have one officer. A 2023 date is old enough that you should ask whether both still apply before you sign. The August 2026 promotion, six free months spread over the first year, ran for sign-ups between 1 and 31 August 2026 per the disclaimer page; if you are reading this later, assume it is gone.
Square Payroll: all 50 states and DC at $41, and a once-a-year health entry
Square Payroll is $35 a month plus $6 per person paid, $41 for one owner, with no contract, auto payroll included and multi-state payroll included, read 30 August 2026. Its help centre lists the forms it files, “Form 941” quarterly, “Form 940, Form 944” annually, W-2 and W-3, and says it “supports payroll tax calculations and filings across all 50 states and the District of Columbia”; new-hire reports go in on request. The gap is question 3. We found no help-centre article on the 2% shareholder premium. The only Square answer is a community thread where Square staff wrote in 2023 that the company “collects S-Corp health insurance premiums at the end of the year” through a year-end checklist, adding them to “Box 1 (Wages), Box 14 (Other), and Box 16” and not to boxes 3 and 5. A moderator in a January 2026 thread declined to give “guidance on tax treatment or payroll setup for owners”. So the mechanism exists, once a year, in December, and it is documented by a forum post, not a product page.
Wave Payroll: the 2% benefit is a named pay item, with a 30-day trial
Wave Payroll is $40 a month plus $6 per active employee, $46 for one owner, with a 30-day trial and a note that these prices apply to customers who signed up after 2 April 2025. It files “in all 50 US states” and lists 940, 941 or 944, W-2 and W-3; it handles new-hire reporting automatically once tax payments are active, and its automatic tax service excludes 1099 filings (the same page says it generates the 1099-NEC; filing it is on you), which matters if you also pay a contractor. Its benefits article, updated 15 June 2026, names “shareholder medical premiums, also known as the 2% Shareholder Health Insurance Benefit” as a pay item and adds that a 2% shareholder cannot receive Section 125 or HSA deductions; the boxes are shown inside the app when you add the benefit, which we could not read without an account. Whether Wave runs payroll without a click each period is not stated on its pages.
QuickBooks Workforce: the built-in item, and the solo owner it sends to Desktop
Intuit’s site would not open from our network on 30 August 2026, so the prices are our 26 August reading, the one on our payroll and accounting round-up: payroll is sold inside accounting bundles, “Workforce Payroll + Simple Start” at $88 a month plus $7 per employee, $95 for one owner, then $135 plus $7 and $228 plus $13 at list. An archive copy of the same page dated 17 July 2026 showed $88 plus $6.50, $125 plus $6.50 and $203 plus $10, so the per-employee fee and two of the three bases rose between mid-July and mid-August, and the 90%-off promotion we saw on 26 August was marked as ending 27 August. Stand-alone payroll plans exist; their list prices were not shown on any of the three readings.
The S corp help article, “Set up an S-corp medical payroll item for your corporate officers”, is thorough and carries the catch of this whole round-up. If the shareholder is on “the same plan as all other employees”, the item is withholding-only and exempt from Social Security, Medicare and FUTA, and Online Payroll supports it under the pay type “S-Corp Owners Health Insurance”. If the shareholder has “a different plan or you don’t offer a plan to employees at all, the plan is fully taxable. This plan type is only supported in QuickBooks Desktop Payroll.” A one-person S corp with no other employee has, on the article’s own wording, no plan offered to employees, which is the second case, and the article says Online does not support it; whether Intuit reads its sentence that way for a solo owner is the question to put to them before you buy. The Desktop instructions name box 14. Ask Intuit which product you are being sold before you take the S corp page’s “reasonable compensation” pitch at face value.
ADP RUN and Paychex Flex: quote-only, with one price in an article
Neither publishes a price. RUN Powered by ADP shows four packages behind “Get pricing” on its 1-to-49-employee page and a promotion of three free months for companies that start processing by 24 September 2026 and stay three months, applied to months four to six. What ADP does publish is a page titled “Payroll for one employee”, “whether you’re an S corporation or another type of one-person business”, and an article updated 5 January 2026 that says ADP “offers a full-service, officer-only S corp payroll solution that starts at $127.95 per quarter ($500 for one-time annual payrolls)”. That is an article’s claim about a product the pricing pages do not show; at four quarters it would be $511.80 a year, and the number belongs to ADP, not to us. ADP’s earnings reference PDF documents an “S-Corp 2% Medical Plan” earning reported “on the employee’s W-2 as federal wages (but not FICA)”, box 1 and box 14 with the code S-CORP, plus separate earnings for an HSA and for Pennsylvania; the PDF is not labelled for RUN specifically.
Paychex Flex lists four packages behind “Request Pricing”, a “Payroll For One Employee” page with no price, and an S corp article last updated 7 November 2024 that describes automatic calculation, payment and filing. The only Paychex document that names the 2% shareholder premium is its 2025 year-end checklist, as an item to verify before 31 December. If a named rep is what you want, both are built for it; if quote-only is the dealbreaker, the Paychex alternatives we priced start from grids.
Collective: payroll inside a back-office bundle, at five to six times the price
Collective is not payroll software; it is a solopreneur back office that includes payroll, “powered by Gusto and synced to your books”. Its plans page on 30 August 2026 shows an S Corp Tier at $349 a month, or “$296/month billed yearly at $3,560” (the page’s own figure; twelve times $296 is $3,552), covering the Form 2553 election, the annual 1120-S, employer registration, “support with reasonable salary” and “member and contractor payroll”, with $15 per additional employee and $5 per contractor in months they are paid. Its help centre says you click “Run Payroll” each period, without autopilot, and that health premiums are added “to your Gusto account as a benefit” by Collective’s onboarding accountant, with COBRA premiums excluded. So the mechanism is Gusto’s, with someone else driving. Price it the way we price stacks in the Year-One Bill: $3,560 to $4,188 a year against $660 for Gusto alone buys the tax return and the accountant, not better payroll.
Deel and Rippling: built for teams, quote-gated for one
Deel’s pricing page on 30 August 2026 lists “Deel Payroll” at $29 per employee per month, US PEO from $125, and contractors at $49, and its US payroll page promises filings “for all 50 states” with W-2, W-4 and new-hire forms; every card ends in “Book a demo”, no minimum headcount is published, and its help centre returned nothing on 2% shareholders. We tested Deel and rate it 8/10 for global hiring and contractors; nothing on its pages says it wants a one-person domestic S corp, and until a quote says otherwise, $348 a year is an “if”; our Gusto vs Deel comparison is where the two meet for a team that is growing, and the EOR and PEO distinction explains what the $125 PEO card buys. Rippling publishes no price at all and no S corp documentation we could find; the Rippling alternatives we priced all print a grid.
The 2% shareholder health premium: what the IRS says, and who names the boxes
This is question 3 in full, because it is the one the vendors want done before 31 December. (The IRS writes “greater than 2-percent”; the vendors shorten it to “2% shareholder”.) The IRS page on S corporation compensation and medical insurance, reviewed 3 March 2026, states that premiums paid for a more-than-2% shareholder-employee “are deductible by the S corporation and reportable as wages on the shareholder-employee’s Form W-2, subject to income tax withholding”, and that they “are not subject to Social Security, or Medicare (FICA), or Unemployment (FUTA) taxes” when paid under a plan for all or a class of employees, so the amount “is included in the shareholder-employee’s Box 1 (Wages) of Form W-2 … but is not included in Boxes 3 and 5”. The Form 1120-S instructions add the reporting line the vendors reproduce: “report amounts paid for health insurance coverage for a more-than-2% shareholder … as an information item in box 14 of that shareholder’s Form W-2”. The 2026 W-2 instructions have since split that box: “box 14 has been split into box 14a and box 14b”, with the old “Other” content in 14a. Notice 2008-1 settles when the plan counts as the corporation’s: when the S corporation pays the premium, or when the shareholder pays it and the company reimburses it in the same year, and either way the premium “must” be reported as wages on that year’s W-2. The reporting is what the owner’s own return hangs on: the same IRS page says a 2-percent shareholder-employee “is eligible for an above-the-line deduction” for the premiums “if the medical care coverage was established by the S corporation”. Two vendor lines belong next to that: Gusto’s article says shareholders who own more than 2% “cannot participate in pre-tax section 125 benefit deductions”, and Wave’s says a 2% shareholder “cannot receive Section 125 or HSA contribution deductions”.
Against that standard: Patriot’s article names box 1, box 14 and box 16; ADP’s reference PDF names box 1 and box 14; QuickBooks names box 14 for Desktop and sends a plan-less solo owner there; Gusto, OnPay, SurePayroll and Wave document the item without naming boxes; Square documents it in a 2023 forum post; Paychex on a checklist; Deel and Rippling not at all. Whichever you choose, the working deadline is the vendor’s: OnPay wants the pay run “on or before December 31” and says a later addition goes through a support ticket, and Square collects the figure in December.
What one employee costs for a year
List prices, one state, one W-2, no promotion, computed from the figures above; the promotions are real but dated, and every one of them expires.
| Tool | Monthly | Year, list | Add back before you compare |
|---|---|---|---|
| SurePayroll Full Service | $36 | $432 | $55 for the year-end forms ($487); $9.99/mo for a second state |
| Square Payroll | $41 | $492 | Nothing published; health premium entered once a year |
| Patriot Full Service | $42 | $504 | $12/mo per additional state (archive copies) |
| Wave Payroll | $46 | $552 | 1099-NEC filing not included |
| Gusto Solo or Simple | $55 | $660 | Multi-state means Plus at $80 + $12 ($92, $1,104) |
| OnPay | $55 | $660 | First month free, so $605 in year one; single-member price unpublished |
| QuickBooks Workforce + Simple Start | $95 | $1,140 | Accounting included; payroll-only plans unpriced |
| ADP RUN, officer-only (article claim) | $127.95 per quarter | $511.80 | A quote decides; the pricing pages show nothing |
| Collective S Corp Tier | $349, or $296 billed yearly | $4,188, or $3,560 as Collective displays it | Tax return and accountant included |
At list, the payroll-only tools with a published price run from $432 to $660 a year, a $228 spread, which is why the documentation column should decide before the price column does. Two billing details for an owner who pays himself quarterly or once a year: OnPay’s help centre charges its per-person fee only for someone paid in the billing period, and Square lists “free seasonal inactivity”; the base fees run every month regardless. If you keep a plain definition of what payroll software does in mind, deposits, returns and forms, every tool above does that part; what separates them is the owner-specific paperwork and what they charge for a second state.
Run the test on the trial, not the brochure
Where a tool lets you set up an account without a sales call, four questions on day one settle most of it. Add yourself as an employee with a monthly salary and look for the auto-run switch. Find the 2% shareholder item, or the benefit, and read what the app says about boxes; if it says nothing, ask support in writing and keep the answer. Add your state and, if you have one, a second state, and read the price change. Then open the tax settings and confirm the tool will file 941 quarterly unless you have an IRS notice for 944 in hand. Ten minutes, on a test we say plainly we have not run ourselves. How we test the tools we do score is on our methods page.
FAQ
What is the best payroll software for an S corp?
The one that passes the Owner-Employee Test at your size, and on the vendors' own pages read on 30 August 2026 that narrows to five: Gusto, Patriot, OnPay, SurePayroll and Wave all publish a price for one employee, file federal and state returns, and document a pay item for the 2% shareholder health premium in their help centres. Gusto is the only one of the five with a plan built for an owner and nobody else (Solo, $55 a month). Patriot is the only one whose article names the W-2 boxes the premium lands in. We have not run an S corp owner's payroll through any of them; we run our own payroll on Gusto and rate it 8/10 for that job.
Does an S corp have to run payroll?
If the owner does more than minor work for the company and takes money for it, the IRS says yes; the one exception it writes, on its Paying yourself page, is an officer "who performs no services or only minor services and who neither receives nor is entitled to receive any pay". Its page on S corporation officers, reviewed 4 July 2026, states that corporate officers are employees for FICA, FUTA and withholding, that "the fact that an officer is also a shareholder does not change this requirement", and that courts have found shareholder-employees subject to employment taxes "even when shareholders take distributions, dividends or other forms of compensation instead of wages". Running payroll means Form 941 each quarter (or Form 944 once a year, but only if the IRS has notified you to file it), Form 940 for unemployment tax, a W-2 and W-3 in January, and your state's returns.
Does Gusto work with S corps?
Yes. Gusto sells a Solo plan for owner-only businesses at $49 a month plus $6 per payroll recipient, which its page rounds to $55, with quarterly 941 filing in all 50 states, a guided Form 2553 election and payroll that runs automatically (read 30 August 2026). Its help centre has an article for marking an employee as a 2% shareholder so that the health premium is taxed correctly, though it does not name the W-2 boxes. One limit in the same article: Gusto does not support an owner who needs both a taxable salary and a non-taxed owner's draw; draws have to be handled outside Gusto. We run our own payroll on Gusto, but we have not run a 2% shareholder item through it.
What is the 2% rule for S corp health insurance?
It is the IRS treatment of health premiums the company pays for anyone owning more than 2% of the stock. The IRS page on S corporation compensation and medical insurance, reviewed 3 March 2026, says those premiums are "reportable as wages on the shareholder-employee's Form W-2, subject to income tax withholding", and are not subject to Social Security, Medicare or FUTA if paid under a plan that covers all or a class of employees. So the amount goes in box 1 and not in boxes 3 and 5; the 1120-S instructions add it as an information item in box 14, which the 2026 W-2 instructions have split into box 14a. Notice 2008-1 says the plan counts as established by the S corporation when the company pays the premium or reimburses the shareholder for it. Six of the twelve tools here document a pay item for this; none of that is tax advice, and the amounts are between you and your accountant.
How do I pay myself from an S corp: salary or distributions?
The IRS answers the order, not the amount. Its compensation page states that S corporations "must pay reasonable compensation to a shareholder-employee in return for services that the employee provides to the corporation before non-wage distributions may be made", and the Form 1120-S instructions repeat that payments to an officer "must be treated as wages to the extent the amounts are reasonable compensation". The IRS lists nine factors it looks at, from training and experience to what comparable businesses pay, and publishes no formula. Gusto's Solo page advertises a reasonable salary calculator and Collective sells "support with reasonable salary"; neither is an IRS number, and this page does not suggest one. Payroll software runs whatever salary you and your accountant set; it does not set it.