Enter your business details to see what each option would cost you. Prices are live from our database and shown in US dollars.
Payroll for an S corp is usually payroll for one person: the owner. An S corporation owner who works in the business is its employee as well as its shareholder, so the salary they draw goes through payroll with tax withheld, the company files quarterly and annual employer returns, and the owner gets a W-2 at year end, exactly as if they had hired someone. Profit on top of that salary is usually taken as distributions, outside payroll. The software's job is the salary half, done on time, every time, at a price that makes sense for a payroll of one. Below are our picks, then a comparison table and calculator set to one employee.
How we chose
We picked for an S corporation whose payroll is mainly or entirely its owner. That puts full-service federal and state filing first, including the quarterly Form 941 and the year-end W-2, because missing a deposit or a return is the same problem for a one-person company as for a large one. Next comes the monthly base fee, which matters far more at a headcount of one than for a larger team, then how well the payroll connects to the accounting software your accountant works in, and finally whether the plan the table costs already covers owner benefits or pushes you up a tier. Plans and pricing checked September 2026, and every price on this page is read live from our database. The table shows each pick's estimated monthly cost at one employee; add people in the Employees field to see how that changes.
What S corps should prioritize
Full-service filing comes first, and it should be on the plan you are actually buying. Gusto's filing row reads Yes, QuickBooks Payroll's Yes, OnPay's Yes and Patriot Software's Yes (Full Service).
Second, the connection to your books. The salary, the employer taxes and the withholding all need to land in the company's accounts correctly, because your accountant works from them when preparing the S corp's return. Gusto's accounting integrations read QuickBooks, Xero, OnPay's QuickBooks, Xero, Patriot Software's QuickBooks, Patriot and QuickBooks Payroll's QuickBooks (native).
Third, owner benefits. Health cover paid for an S corp owner is reported differently on the owner's W-2 from an ordinary employee's, so if you plan to run owner health cover or retirement contributions through the company, ask your accountant how they should be reported and check the payroll software can record them. On benefits administration, OnPay's row reads Yes, Gusto's Yes, QuickBooks Payroll's Yes and Patriot Software's Limited.
Reasonable salary, and what payroll software does not decide
The rule that shapes S corp payroll is that an owner who works in the business should be paid a reasonable salary for that work before taking profit as distributions. The IRS looks at what the owner actually does, and at what the business would pay someone else to do it. None of the software here sets that figure for you: every one of them will process whatever salary you enter, withhold correctly from it and file the returns. That is the right division of labor. Decide the salary with your accountant, write it down with the reasoning, and let the payroll software run it on a regular schedule so the company's records show a salary paid consistently through the year.
S corp payroll filings, quarterly and year-end
Once the salary is running, the employer filings follow a fixed calendar. Each quarter, the S corp generally files Form 941 reporting the income tax, Social Security and Medicare withheld and owed. Each year it generally files Form 940 for federal unemployment tax, issues the owner's W-2 and sends the transmittal Form W-3. Alongside those sit your state's withholding and unemployment returns, on the state's own schedule. Full-service payroll prepares and files each one and makes the tax deposits between them, which is most of what you are paying for with a one-person payroll. Filing obligations vary with your state and your circumstances, so confirm yours with your accountant. Every pick here files year-end forms: Gusto's row reads Yes, QuickBooks Payroll's Yes, OnPay's Yes and Patriot Software's Yes.
The verdict
Gusto ($49/mo plus $6/emp/mo) is the all-round choice for an owner-employee who wants full-service filing on every tier and room to add staff. QuickBooks Payroll (sold mainly alongside a QuickBooks Online plan, with the figure we hold in the table) is the fit when the company's books already live in QuickBooks Online. Patriot Software ($37/mo plus $5/emp/mo) suits a lean payroll that is one owner's salary and nothing else. OnPay ($49/mo plus $6/emp/mo) suits an S corp that runs owner benefits through payroll on a single plan. The table above shows what each costs at one employee today.
If your first hire is someone other than you, see our guide to the best payroll software for one employee. Once the company has a small team, see the best payroll software for small business.