Overview

Running payroll means turning work into accurate, on-time pay every period. This guide walks U.S. employers through a compliant, vendor-neutral workflow for 2025, from setup and gross-to-net calculations to tax deposits, filings, and day-to-day operations.

It’s designed for small-to-midsize employers and payroll admins who need a clear process that works regardless of software or bank.

What does it mean to run payroll?

To run payroll is to collect hours and earnings, calculate gross-to-net pay, disburse wages, and handle taxes and reporting. In practice, that includes time capture, overtime and deductions, tax withholding, pay stubs, and tax deposits.

You’ll work on a fixed payroll schedule. Each pay period covers the work dates. The pay date is when employees receive wages. For W-2 employees, you withhold income and FICA taxes and issue pay stubs. For independent contractors, you generally pay outside payroll and do not withhold taxes. The run is complete only when net pay is delivered and tax deposits are scheduled or made.

Why do timing and accuracy matter when you run payroll?

Because late or inaccurate payroll erodes trust and can trigger penalties, timing and accuracy are essential. Wage-and-hour laws and tax deposit schedules create legal and financial risk for employers who miss deadlines.

The Fair Labor Standards Act (FLSA) requires at least minimum wage and overtime at 1.5× the regular rate for hours over 40 in a workweek; see the U.S. Department of Labor’s FLSA overview for details. State pay frequency rules and bank/ACH timelines also affect your cutoff planning. A single missed overtime premium or late payday can lead to back pay, fees, and fix-up work. Build a tight approval cadence and a calendar that accounts for bank holidays. Set your payroll calendar now, then work backward from the pay date to your approval cutoff.

What do you need in place before your first pay run?

You need your employer and employee tax setup, payment rails, and a clear process for time, approvals, and changes. Get registrations, forms, and banking ready before the first run to avoid delays.

Once these are in place, run a dry run (no disbursements) to validate calculations and funding before your live payday.

Which payroll setup options should you choose?

Choose a pay frequency, payment method, and processing approach that fit cash flow, staff needs, and state requirements. The right mix depends on your workforce composition and operational capacity.

Pay frequency is governed by state law in many jurisdictions, so ensure your schedule meets state minimums. Direct deposit reduces errors and costs versus paper checks, but you must plan for ACH lead times and offer alternatives for employees without bank accounts. Paper checks or pay cards (where allowed) are common options. You can process payroll in-house or with a provider: in-house offers control but requires expertise, while providers automate taxes and filings. Also define accrual policies (PTO/sick), overtime rules, and approval cutoffs so supervisors and employees understand the timeline. For example, a seasonal retailer might use weekly payroll during peak months and biweekly the rest of the year, with direct deposit as the default and checks for new hires without bank details.

How much does it cost to run payroll?

Expect recurring software and per-employee fees, plus banking and payment costs. Complexity—like multi-state payroll or garnishments—adds administrative time and provider fees.

Taxes withheld and employer taxes (e.g., FICA, FUTA, SUTA) are liabilities you remit, not service fees. Build both cash funding for net pay and tax liabilities into your payroll calendar.

What are the step-by-step actions to run payroll each pay period?

Follow a consistent sequence: gather data, calculate gross-to-net, pay employees, and deposit taxes. A stable sequence reduces errors and simplifies audits.

This sequence keeps your payroll run predictable, auditable, and aligned with regulatory requirements.

How do you calculate gross-to-net correctly?

Calculate net pay by starting with gross earnings, subtracting pre-tax deductions, withholding taxes, then applying post-tax deductions and garnishments. Employer taxes are calculated in parallel and funded by the company.

Begin by listing earnings (hourly, salary, overtime, tips, commissions, shift differentials) and subtracting pretax items that reduce taxable wages. Withhold federal, state, and local taxes using IRS Publication 15-T methods (wage bracket or percentage) according to each employee’s Form W-4 elections, and then apply post-tax deductions and garnishments. Be precise about what is pre-tax (e.g., certain health or retirement deferrals) versus post-tax (e.g., Roth contributions), since that affects the taxable base. If you process tips or supplemental wages (bonuses), follow the methods described in Publication 15-T to determine withholding.

How long does direct deposit take and when should you approve payroll?

Standard ACH payroll typically requires about 2–3 business days for funds to post; Same Day ACH can be faster but has limits and cutoff windows. Many providers require approval 2–4 business days before payday to meet bank processing schedules.

Plan approvals backward from the pay date, accounting for bank holidays and weekends. If payday falls on a bank holiday or weekend, most employers move the pay date to the prior business day to ensure access to funds. See NACHA’s Same Day ACH overview (https://www.nacha.org/same-day-ach) for timing and limits. For employees without bank accounts, use paper checks or payroll cards where permitted and build print/distribution lead times into your cutoff.

How do you handle ongoing payroll operations and changes?

Maintain a standing process for off-cycle runs, terminations, bonuses, garnishments, benefits changes, and multi-rate jobs. Clear documentation and approval routes keep recurring and exceptional flows consistent.

A simple change log tied to each pay period helps you show what changed, when, and who approved it.

How do you correct a payroll mistake after submission?

Act quickly to stop or reverse erroneous payments, then correct taxes and records. If reversal isn’t possible, correct on the next payroll or with an off-cycle payment and document the fix.

Many banks and providers support ACH reversals or returns within a limited window; if funds cannot be recovered, issue an adjustment in the next run and update the employee’s year-to-date records so W-2 reporting remains accurate. If federal tax amounts already reported for a quarter need correction, you may need to file an amended 941 series return; see the IRS Form 941 guidance (https://www.irs.gov/forms-pubs/about-form-941). Communicate clearly with affected employees about what changed, when it will be corrected, and how it will appear on their pay stub.

How should you handle multi-state employees and local taxes?

Register where you have withholding and unemployment obligations, and set the correct state and locality codes in payroll. Accurate registration and coding ensure correct withholding, deposits, and filings.

You generally need state income tax withholding accounts and state unemployment (SUTA) accounts where employees work; start with the FTA’s state tax agency directory (https://www.taxadmin.org/state-tax-agencies) and the DOL’s UI agency directory (https://oui.doleta.gov/unemploy/agencies.asp). Account for reciprocity agreements, local taxes, and state-specific rules. Keep a state-by-state matrix of rates, employer IDs, deposit schedules, and filing frequencies so changes are deliberate and auditable each run.

How do you measure payroll accuracy and efficiency?

Track a handful of KPIs monthly to catch issues early and improve continuously. Simple metrics make errors visible and help predict workload around holidays and quarter close.

Review these alongside your calendar. Spikes often correlate with holidays, staffing changes, system changes, or large bonus runs.

What common pitfalls should you avoid when you run payroll?

Most payroll issues stem from timing slips or missing setup; preventing those two categories will avoid the majority of problems. A short prevention list can save hours of rework and employee frustration.

A pre-payday review checklist and a holiday-adjusted calendar will prevent most of these pitfalls.

What are your next steps to stay compliant throughout the year?

Maintain deposit schedules, file required returns on time, and reconcile year-to-date totals before year-end. Establish a lightweight annual rhythm to surface rate changes and preview reporting early.

Federal employment tax returns in the 941 series are due quarterly; FUTA is reported annually on Form 940. Forms W-2/W-3 are generally due to the Social Security Administration by January 31; e-file through SSA Business Services Online (https://www.ssa.gov/employer/). Confirm SUTA and local rate changes each January, validate employee addresses and state/local codes after moves, and preview W-2 totals in November and December. Archive payroll registers, tax receipts, and approvals each period, and securely store records with clear access controls. If you switch providers mid-year, migrate complete year-to-date earnings, taxes, and deduction totals so quarter and year-end forms remain accurate across systems.