How Much Does S Corp Payroll Cost? DIY, Payroll Apps or Done for You

Most cost guides only compare app prices. For an S corp owner, the real cost has four parts: the service fee, the payroll taxes the company owes on your salary, the state accounts you need before the first paycheck, and the cost of a missed deadline. This guide prices each one, using published rates and pricing pages, so you can compare running it yourself, using a payroll app and handing it to a payroll team.

Here is the short version for a single-owner S corp paying one salary:

• Run it yourself: $0 in service fees. You pay with your time each month and quarter, and you carry the risk if a deposit or return is late.
• Payroll app: about $250 to $660 a year at the list prices below. The app calculates and files most returns, and you still handle setup, state accounts and changes.
• Full-service payroll team: PayAdvisors quotes its S corp payroll package on a quick consultation, based on what your payroll needs. A team registers your state accounts, runs your salary, files every return and issues your W-2.

Whichever you choose, the company’s share of payroll taxes on your salary is the same. That is usually the largest number, so it comes first.

Once you pay yourself a salary, the S corp is an employer and you are its employee. The company withholds your share of taxes from each paycheck and pays its own share on top:

• Social Security: 6.2% from the company and 6.2% withheld from you, on wages up to the 2026 wage base of $184,500.
• Medicare: 1.45% from the company and 1.45% withheld from you, with no wage cap. Wages over $200,000 also carry a 0.9% Additional Medicare tax that is withheld from the employee only, with no employer match.
• Federal unemployment (FUTA): 6.0% on the first $7,000 of each employee’s wages. If you pay your state unemployment tax in full and on time, the credit of up to 5.4% usually brings the net rate to 0.6%, or $42 a year per employee. Employers in a credit reduction state can owe more.
• Federal income tax: withheld from your paycheck based on your Form W-4. It comes out of your salary, so it is not an extra company cost.

For example, on a $60,000 owner salary the company’s share of Social Security and Medicare is $4,590 (7.65%), plus about $42 of FUTA at the net rate. The same $4,590 is withheld from your paycheck. Your CPA sets the salary; the IRS expects an S corp to pay a shareholder who works in the business reasonable compensation before taking distributions.

These costs depend on where you live and work, which is why most price lists leave them out:

• State unemployment insurance: each state sets its own rate and taxable wage base, and new employers usually start on an assigned new-employer rate.
• State income tax withholding: states with an income tax generally require a withholding account before your first paycheck. It does not add a company tax, but it adds returns to file.
• Workers’ compensation: whether an owner who is also an officer must be covered, or can opt out, depends on the state. Check with your state’s workers’ compensation agency or your insurance agent.
• Registration: you can open the state accounts yourself, but the forms and timing differ by state. With PayAdvisors, registration in your home state is included in the S corp payroll package. Pricing for any additional state or other added registration depends on the states and accounts involved, and a dedicated tax manager handles it.

Our state payroll tax registration guides cover the agencies, forms and 2026 rates for 20 states.

Doing it yourself has no service fee. Federal deposits go through EFTPS, a free Treasury system. What you take on is the calendar:

The real cost of doing it yourself is the cost of getting it wrong. A late federal deposit draws a failure-to-deposit penalty of 2% at 1 to 5 days late, 5% at 6 to 15 days and 10% after that, rising to 15% if it is still unpaid more than 10 days after the first IRS notice. A late W-2 is penalized per form: for returns due in 2026, $60 up to 30 days late, $130 through August 1 and $340 after that or if never filed, and the IRS charges a separate penalty for the copy you owe the employee.

If you have already missed a run, our guide to forgotten S corp payroll walks through the catch-up.

Payroll apps charge a monthly base fee plus a fee per person paid. For a one-person S corp, the list prices we checked on October 27, 2026 were:

• Gusto Solo: $49 a month base plus $6 a month per payroll recipient, which Gusto says is $55 a month for most owners, or $660 a year.
• Patriot Full Service Payroll: $37 a month plus $5 per worker paid, or $42 a month ($504 a year) for one person. It includes federal, state and local tax filings and deposits.
• Patriot Basic Payroll: $17 a month plus $4 per worker paid, or $21 a month ($252 a year). You file and deposit the taxes yourself.

Promotional discounts can lower the first months. Add-ons cost extra: Gusto, for example, lists state tax registration as an add-on with pricing that varies by state. With an app, you still own the setup, the state accounts, any salary change your CPA recommends, and the agency letters that arrive when something does not match.

Full service means a payroll team does the work instead of you. It costs more than an app, and you stop being the person who has to remember every deadline.

PayAdvisors’ S corp payroll package is quoted on a quick consultation, based on what your payroll needs. Registration in your home state is included in the package. Pricing for any additional state or other added registration depends on the states and accounts involved. Month to month, with no minimum term. It covers:

• Registering your state withholding and unemployment accounts, in your state and any other state where you work
• Running your salary every month, with your approval on each run
• Every federal and state deposit and return
• Your year-end W-2

What it does not change: your CPA still sets your salary and files your S corp return. You never log in to a payroll system.

Run it yourself

• Yearly service fee: $0
• Your time: every payday, every quarter and year end
• Who files: you
• Who fixes mistakes: you

Payroll app

• Yearly service fee: about $250 to $660 at the list prices above, plus any add-ons
• Your time: setup, state accounts, changes and notices
• Who files: the app, for the returns its plan covers
• Who fixes mistakes: you, with the app’s support team

Full-service payroll team

• Yearly service fee: quoted on a quick consultation, based on what your payroll needs. Home-state registration is included
• Your time: approving each run
• Who files: the payroll team
• Who fixes mistakes: a dedicated payroll team works it through with you

The payroll taxes on your salary are the same in all three. The difference is the fee, your hours and who is responsible when a deadline comes up.

Run it yourself if

You already know employment tax deposits and returns, your salary rarely changes, and you are comfortable owning every deadline.

Use a payroll app if

You want the calculations and filings automated, you are happy to handle setup and state accounts, and you would rather pay the lowest fee.

Hand it to a payroll team if

You do not want to think about payroll at all, you are setting up in a new state, you are switching from an app mid-year, or you have missed a run before and want someone else watching the calendar.