Payroll Software for Trucking Companies

Trucking payroll breaks the assumptions most small-business payroll is built on. Drivers are often paid by the mile or by the load rather than by the hour, many work a long run away from home with a per diem for meals, some are employees and some are owner-operators on 1099s, and the overtime rules are not the usual ones. A payroll service for a carrier has to take all of that without workarounds. We read the IRS, Department of Labor and provider pages on October 28, 2026. Nothing here is tax or legal advice for a particular fleet, and nothing comes from a hands-on trial.

For whom: a carrier or fleet with 2 to 50 drivers, mixing W-2 drivers and 1099 owner-operators. Not for: a fleet that settles owner-operators through dispatch or TMS software and needs payroll only for office staff; any of the services on our small business list will do.

Three rules payroll has to get right

1. Per diem. For travel on or after October 1, 2026, IRS Notice 2026-60 sets the special meal and incidental rate for the transportation industry at $80 a day for travel in the continental US and $86 outside it; the incidental-expenses-only rate is $5. Publication 15 for 2026 says a per diem paid under an accountable plan is treated as substantiated up to the federal rates, with the other elements of the travel still substantiated; a per diem within that amount is generally not wages. When the allowance exceeds the substantiated amount, the excess is wages and taxed, and the 2026 Form W-2 instructions say to use code L in box 12 only in that case, reporting there the substantiated, nontaxable part. Example: a driver away five days receives $90 a day; at $80 the substantiated part is $400 and the remaining $50 is wages.
2. Overtime. Under section 13(b)(1) of the FLSA, as the Department of Labor's Fact Sheet 19 explains, drivers, helpers, loaders and mechanics employed by a motor carrier whose duties affect the safety of vehicles in interstate commerce are exempt from overtime, except that the small vehicle exception restores overtime in a workweek in which they work on vehicles of 10,000 pounds or less, with exclusions for certain passenger vehicles and vehicles carrying placarded hazardous material. A mixed fleet needs a way to flag those weeks.
3. Employees and contractors. Owner-operators paid on a 1099 are not on the W-2 run, and a tool that pays both in one run spares a second process. A 1099 setting in software does not make a driver a contractor: under the IRS general rule, a worker is an independent contractor only if the carrier controls just the result of the work, not what is done and how, and the facts of each case decide. So set up as contractors only drivers whose status you have already determined.

What each provider documents

Our pick

OnPay. It is the only one of the three whose own page describes trucking pay as it is actually run: custom rates per mile, per load or per hour, W-2 drivers and 1099 owner-operators in the same run, multistate payroll included and new-hire reporting it calls "DOT-friendly". A carrier can price it before talking to anyone.

• Choose RUN Powered by ADP if you want a payroll specialist reachable at any hour, which matters when settlements run late at night, and accept a quoted price. Its getting-started guide documents renamable earnings, not per-mile calculation or per diem reporting, so get ADP's written confirmation of both workflows before the first run.
• Choose Patriot if your accountant runs payroll and wants to define each pay item's taxability: its money types allow custom tax settings; the help article we read does not document per-mile calculation, so confirm the workflow with Patriot.

Before your first run

Ask whichever provider you choose two questions in writing: how it reports a per diem that exceeds the substantiated amount (excess as wages, nontaxable part in box 12 code L), and how it lets you mark a workweek that falls under the small vehicle exception. If either answer is "manually", keep a checklist next to each run. For contractor setup, see payroll for employees and contractors.