How Much Does Payroll Software Cost

Payroll software pricing for a small team depends on several variables, including the number of employees, pay frequency, and tax filing scope. Your base fee is only part of what you'll pay.  

Understand how those variables interact and you can evaluate any pricing page with confidence.

SurePayroll By Paychex pricing is built the same way: base fee, per-employee rate, and full-service tax filing available.

What determines the cost of payroll software

Team size, pay frequency, and tax filing scope drive most of what you’ll pay to outsource payroll with software.  

Team size

Most providers charge a flat monthly base fee plus a per-employee fee each pay period. You pay less for a team of three than a team of eight on the same plan, every month.  

Pay frequency

How often you pay your team can influence your monthly total.  

Some payroll service providers charge per payroll run. This means running payroll every week will cost twice as much as bi-weekly over the course of a year.  

If you manage hourly staff on variable schedules and need flexibility in your pay period, per-run pricing adds up fast.  

Other providers offer unlimited payroll runs, so your payroll frequency doesn’t impact your monthly cost.  

Confirm how the per-run pricing is structured before you sign up.

Tax filing scope: full-service vs. basic payroll

This is the biggest cost variable in small business payroll.  

Basic payroll calculates paychecks, including payroll taxes and deductions, and handles direct deposit.  

With full-service payroll, you get everything in basic. The software also automates tax deposits plus federal and state filings.  

Full-service costs more per month. In exchange, you avoid time-consuming payroll administration after every run.

Two costs to confirm before you commit

If you pay employees and independent contractors, confirm the plan can handle both.  

If you have employees or contractors in more than one state, confirm multi-state coverage before you start.  

What the base price covers and what costs extra

Most pricing pages lead with two numbers: the monthly base fee and the per-employee rate. Your monthly total depends on more.

Year-end forms

What you pay for W-2 and 1099-NEC preparation and filing depends on your plan.

Some full-service plans include it in the base price. Others bill it as a per-form fee each January. Check whether the pricing page shows it up front or bills it at year-end.

Off-cycle and bonus runs

On plans that charge per run, you pay a fee every time you correct a paycheck, issue a bonus, or process off-cycle payroll.  

If you issue bonuses or run corrective payroll more than once a year, a plan with unlimited runs will cost you less.

Add-ons

Time tracking, benefits administration, workers’ compensation coverage, and health insurance integrations add to your monthly total. If you need any of them, check the cost before you commit. They won’t appear in the base fee.

Multi-state payroll

Most plans don’t share the additional fee on the main pricing page. Some include it in the base price. Others charge per state. Confirm which applies and what it costs before you sign up.  

Contractor payments

Not every plan supports employees and independent contractors in the same system. Some charge extra for contractor payments or year-end 1099-NEC forms. Before you sign up, confirm which applies.

Other fees to ask about

Watch for onboarding or setup fees, paper paycheck fees, or tiered customer support access. If a pricing page doesn’t address them, ask before you sign up.

Small business owners without automated payroll spend an average of five hours a month on payroll administration, according to the National Small Business Association. That cost doesn't appear on any pricing page.

See how automated payroll software for small business can save time and money

What you buy with full-service payroll

With a full-service payroll solution, the software calculates your payroll tax liability, makes the deposits, and files the required forms on your schedule. With a basic plan, you make the deposits and you file the forms yourself.

After each payroll run on a basic plan, you take the calculated figures and schedule the deposits with the IRS and your state tax agency yourself, track the required deposit deadlines, and file the quarterly and year-end forms: Form 941 each quarter, Form 940 annually, W-2s and 1099-NECs at year-end.

Learn how to fill out form 941.

A full year of full-service coverage is more cost-effective than a single failure-to-deposit penalty on a modest quarterly bill. The IRS applies the same deposit rules to a two-person team as it does to a corporation. Penalties start at 2 percent for deposits one to five days late and scale to 15 percent after the first IRS notice.

Basic payroll also costs you time.  

Before switching to SurePayroll, 42 percent of small business owners said time spent on payroll was their top concern, and 38 percent named fear of making mistakes in a 2025 survey. Full-service payroll addresses both: the software calculates, deposits, and files your taxes on your schedule, and you reclaim the hours you'd spend managing the deposit cycle.

“[SurePayroll] provides options and features that much more expensive software didn't have.”  - Joseph, Capterra review

What payroll software costs for a team your size

A January 2026 survey of publicly available pricing across major payroll providers puts a full-service plan for a two-employee, one-state business at $588 to $1,000 or more per year. The range reflects plan structure: some include year-end forms and unlimited runs in the base price; others price them separately.

Full-service plan cost at SurePayroll costs at SurePayroll

SurePayroll By Paychex is built for small teams. A full-service plan for a two-employee, one-state business costs $516 per year: a flat monthly base fee plus a per-employee rate. The base price includes full-service tax filing, direct deposit, and unlimited payroll runs.

You run W-2 employee and 1099 contractor payments through the same dashboard and generate year-end forms for both in the same system.

See your monthly SurePayroll price.  

Switching from manual in-house payroll to online payroll cuts average payroll processing pricing by 80 percent, according to a Paychex 2022 survey of 1,000 HR decision-makers, accounting for time, processing fees, and error-related hidden costs. The monthly fee for software is one number.  

Price the full picture before you decide.

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Ask these questions before you commit to a plan

Use these six questions with any payroll provider before you sign up to surface what pricing pages don’t show.

Does the base price include full-service tax filing?

Basic and full-service plans often carry similar-looking base fees. Confirm whether the plan covers tax deposits and filings or whether you’re responsible for managing them.

Are payroll runs unlimited?

On per-run plans, you will pay a fee for every off-cycle or bonus payroll. You avoid that variable entirely if you choose a service with unlimited payroll runs. This matters most if you manage hourly staff on variable schedules or process payroll off-cycle for bonuses, commissions, or expense checks.  

What are the year-end form fees?

Ask whether the base price covers W-2 and 1099-NEC preparation and filing or bills them as a per-form fee each year. Get the specific amount before you commit. If the pricing page doesn’t address it, ask directly.

Does the plan cover both W-2 employees and 1099 workers?

Confirm you can pay both worker types in the same system. Ask whether the plan includes 1099-NEC generation or prices it separately. You will add cost and administrative work at year-end if you run two separate systems.

What does multi-state payroll cost?

If you have remote employees in other states, confirm the plan covers the additional state tax filings and at what price. If you’re adding remote hires, price it in before you sign up.

What add-ons are available and what do they cost?

Time tracking, benefits administration, and workers’ compensation integrations are common additions to a base plan. Price them upfront so you know what you’ll pay.

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See what SurePayroll costs for your team

SurePayroll is built for small teams. Full-service tax filing, direct deposit, and unlimited payroll runs. See exactly what you get and what it costs, then decide.

See pricing and features

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