ABA Timesheet Software: Payroll, Billing and Time Tracking for Canadian Clinics

Quick answer: ABA time tracking is harder than ordinary payroll because one technician can work several clients at several rates in one day, with travel between them. In Canada that creates two specific obligations most generic tools miss: Ontario’s ESA requires you to record hours worked above the overtime threshold at each rate of pay, and CRA mileage reimbursement is only tax-free if it’s per-kilometre and properly logged.

The Sunday Night Spreadsheet

Every clinic operator I’ve spoken to has a version of this story.

Ours involved a Sunday evening, a laptop, eleven technicians, and a spreadsheet with a tab per person. Someone had logged a full afternoon against the wrong client. Someone else had recorded travel as therapy time. Two mileage claims had no destinations attached.

None of it was carelessness. It was a system that asked people to remember things at the end of a long week.

What finally changed things wasn’t better discipline. It was accepting that if the record isn’t captured at the moment the work happens, it will be reconstructed later — and reconstructed records are wrong records.

Why ABA Time Tracking Isn’t Ordinary Time Tracking

One person, several clients, one day. A technician may see four or five children between morning and evening. Each session ties to a different file, a different plan, and often a different funding source.

Several rates for one employee. Direct therapy, supervision, assessment support, and travel are frequently paid at different rates. That single fact breaks most off-the-shelf tools, and as you’ll see below, it also carries a specific legal record-keeping consequence in Ontario.

Travel that isn’t commuting. Driving from your home to your first client generally isn’t paid time. Driving from client one to client two generally is. Distinguishing those two things reliably, every day, across a team, is where manual systems fail first.

Documentation that has to survive scrutiny. Funders, insurers, and auditors all ask for records after the fact — sometimes long after.

The Canadian Compliance Layer

This is the part software vendors rarely explain and generic tools weren’t built for.

Overtime is weekly, not daily. Under Ontario’s Employment Standards Act, 2000, overtime is owed at 1.5× after 44 hours in a work week. There’s no daily trigger — a 12-hour day isn’t overtime unless the week exceeds 44.

Paid travel time counts toward that threshold. Travel that qualifies as work time is hours of work under the ESA, meaning it pushes technicians toward 44 hours. A clinic tracking therapy hours but not travel hours can be understating overtime liability without realising it.

Multi-rate employees have an extra recording obligation. Where an employee has two or more regular rates of pay and works beyond the overtime threshold in a week, the ESA requires the employer to record the dates and times worked in excess of the threshold at each rate of pay. For ABA clinics — where different rates are the norm — this is the single most commonly missed requirement, and it cannot be reconstructed from a total-hours spreadsheet.

Retention periods differ by record type. Most ESA records must be kept for three years; vacation time and pay records for five. Records also need to be readily available for inspection, not buried in an archived system.

Employees can generally pursue unpaid overtime going back two years through an ESA complaint. Your records are the defence.

Mileage: Getting the Tax Treatment Right

For 2026, the CRA’s reasonable per-kilometre allowance is 73¢ for the first 5,000 business kilometres and 67¢ thereafter, with an additional 4¢ in the Northwest Territories, Yukon, and Nunavut. Confirm the current figure before setting your rate — it moves annually.

Two things follow from this, and they matter financially:

Per-kilometre reimbursement within the prescribed rate is not taxable. It isn’t subject to CPP or EI deductions and isn’t reported as income on a T4.

A flat monthly car allowance generally is taxable. Because it isn’t tied to documented business kilometres, it typically fails the CRA’s reasonableness test and becomes income — with withholding obligations attached.

Which means the logbook is the whole thing. CRA expects each business trip to record the date, destination, purpose, and distance driven. “1,400 km this month” is not a record. If your timesheet system can’t capture those four fields per trip, it isn’t solving your mileage problem.

Your Service Model Determines Your Requirements

This is where clinics buy the wrong tool. The right system depends on how you actually deliver.

In-home programmes generate the heaviest travel load. Skills are taught where they’re used — which is why we deliver ABA therapy at home in Canada — but it means every technician’s day contains multiple trips needing per-trip capture, not a daily total.

Virtual delivery removes mileage entirely and replaces it with a different problem: session-level verification. Virtual autism therapy in Canada needs start and end times tied to the right file, because there’s no physical arrival to anchor the record.

Assessments sit under separate service categories from ongoing therapy, often at different rates and with different documentation standards. If children’s assessments run through the same undifferentiated time field as therapy hours, your reporting will misstate both.

A clinic running all three — as we do across our home based ABA therapy services in Canada — needs a system that treats them as genuinely different things.

What to Look For

Evaluate against your actual obligations, not a feature list:

• Session-level entry tied to client, date, duration, and service type — not daily totals
• Multiple pay rates per employee, with hours above the overtime threshold recorded separately by rate
• Per-trip mileage capture with date, destination, purpose, and distance
• Billable travel time recorded distinctly from mileage — they’re different entitlements
• Submission and approval workflow with a visible audit trail
• Retention that meets three- and five-year requirements, exportable on demand
• Payroll export that doesn’t require manual re-entry

Purpose-built options exist — ABA Timesheet is one platform designed around these workflows, with Canadian payroll in mind. Whatever you choose, test it against the multi-rate overtime scenario before committing. That’s where most tools fail.

The Connection to Clinical Data

Administrative records and clinical records answer to different masters, but they share a principle: recorded at the time, or effectively lost.

The same discipline that makes payroll defensible makes progress measurable. Our guide to data collection in autism therapy covers the clinical side of that equation.

Frequently Asked Questions

Is travel time paid in Ontario? 

Travel that qualifies as work time — typically between client locations during the workday, rather than the initial commute from home — counts as hours of work under the ESA and contributes to the 44-hour overtime threshold.

What mileage rate should we reimburse? 

The CRA’s 2026 reasonable rate is 73¢/km for the first 5,000 km and 67¢/km after, plus 4¢ in the territories. Paying within it keeps reimbursement non-taxable, provided trips are properly logged.

Can we pay a flat monthly vehicle allowance instead?

 You can, but it’s generally treated as taxable income because it isn’t tied to documented kilometres — which usually makes per-kilometre reimbursement the better arrangement for both sides.

How long do we need to keep timesheet records?

 Most ESA records require three years; vacation time and pay records require five. Records must be readily available for inspection.

Do we need ABA-specific software, or will a general tool work? 

The deciding test is multi-rate overtime recording and per-trip mileage. If a general tool handles both cleanly, it may be sufficient. Most don’t.