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How to Set Up an Online Payroll Account in Canada

When you start your business, your team may just be you. However, as you grow and onboard employees, your payroll needs will expand, and you’ll need a quality online payroll system.

If this is your first time implementing payroll online, there is a lot to learn. However, with support from experts like the QuickBooks Resource Centre, and the Canada Revenue Agency, your payroll will run smoothly.

Review each step you need to follow to set up online payroll, calculate deductions, and maintain your accounting records using QuickBooks in a clear and easy-to-follow manner so that you can tackle the tasks with ease and confidence. 

If you are in Québec, you will need to register your business with the Canada Revenue Agency (CRA) and Revenue Québec (RQ) to remit payroll to both. You will have to send the QPP, QPIP, and Québec provincial income tax deductions to Revenu Québec.

What do you need to set up payroll online?

Before you open a payroll account with the CRA, you must first register a business number (BN) for your organization. A business number is a unique nine-digit number that identifies businesses matters with federal, provincial, and local governments. The CRA uses your BN to identify your company for all tax matters related to your business, including earnings and payroll taxes.

Your BN identifies your business when you register with any of the four major government programs outlined below:

  • Goods and services taxes/harmonized sales taxes (GST/HST)
  • Payroll deductions for employees
  • Import-export
  • Corporate income tax.

For each program account, your business receives a 15-character account number. The first nine digits of the account number are your BN. Next, a two-letter acronym identifies the program. Lastly, a four-digit number references the specific account. If you sign up for payroll online, then your BN will have the initials RP. Below is a guide to Canadian business numbers:

  • RT for GST/HST accounts
  • RP for payroll accounts
  • RM for import-export accounts
  • RC for corporate income tax accounts

All sole proprietors, partnerships, corporations, trusts, and other ownership types receive an individual BN. You use your BN for all your company’s dealings with the agency, so memorize it or keep it close at hand.

If you are in Québec, you need to register with CRA for a CRA business number and with Revenu Québec for a Quebec enterprise number (NEQ) as you have to send the the CPP, EI and federal tax deductions to the CRA and QPP, QPIP, and Québec provincial income tax deductions to Revenu Québec.

For details, check Registering with Revenu Québec or use the service by Revenu Québec to Register a new business.

Registering for the Payroll Program

When setting up online payroll, it’s essential to know your first remittance due date. The remittance due date is the date your company sends information or payments to the CRA. Knowing your remittance due date to submit payroll deductions ensures that you register on time and avoid penalties for late remittance.

Your first remittance due date is the 15th day of the month following the month you begin withholding deductions from your employee’s pay.

Example 1

Imagine you hire an employee on March 11, and you decide to pay them bi-weekly. You make the first payment on March 25, so your first remittance due date is April 15.

Example 2

If you hire an employee on March 25 and pay them on April 3, then your first remittance due date is May 15.

Even if you don’t open an account with the payroll program before hiring your employees, you still need to calculate deductions and remit them by the proper due date. If you fail to deduct or you send remittance beyond the due date, the CRA may assess a penalty.

Gathering the Information to Register For Online Payroll

Preparing all the necessary information in advance to register for online payroll with the CRA helps the process go smoothly. Start by gathering the following information needed to register for your payroll account:

  • Social Insurance Number (SIN) Income tax return filed with the CRA
  • Basic personal information
  • Basic business information including your BN (and NEQ if in Québec)
  • If incorporated, you need your corporate name, certificate number, date of incorporation, and jurisdiction

Once you have a payroll program account you need:

  • The date employees receive their first wages
  • Months covered for payroll of employees’ wages
  • The type of pay period (example: weekly, quarterly)
  • The number of employees
  • Payroll service name (if any)
  • Country of parent or affiliate (if you have a foreign-owned corporation)
  • Name of franchiser and country of franchise’s head office (if any)

How to Register for an Online Payroll Account

You can register for a BN and your CRA program accounts in any of the following ways:

If you plan to register by phone, via mail, or through fax, you need to complete a request form.

If you are in Québec, you will also have to register for source deductions with Revenu Québec.

Hiring Your First Employee and Calculating Remittance Amounts

Once you have your BN (and NEQ if in Québec) and register your online payroll account with the CRA, you can hire new employees and calculate the appropriate deductions required for remittance on behalf of each employee. To get started, you need the Social Insurance Number of the employee; then you need to file a TD1 Personal Tax Credits Return.

The Personal Tax Credits Return form determines how much tax to deduct from an individual’s employment income. You don’t need to submit either the federal or provincial form to the CRA, but the employee needs to complete the forms, and you need to keep them on file in your offices.

You can ask employees to fill out paper copies, or they can use an Electronic Form TD1 and provide you with a printed copy. Most employees only need to fill out this form once, at the start of their employment.

They only ever need to submit a new form if they need to make a change to federal and/or provincial tax credit amounts or want to increase the amount of tax you deduct from their pay cheques.

To help you determine how much tax to remit for your employee, the Personal Tax Credits Return form takes into account the employee’s dependents and other items that affect how much tax the employee owes. The more accurate the information your employee provides, the fewer corrections there are at tax time.

The form asks your employee to estimate the following:

  • Annual net income
  • Annual pension income
  • Annual tuition fees
  • Dependents’ ages and net income
  • Spouse or common-law partner’s net income
  • Amounts your dependent(s) use on their income tax and benefits return
  • Amounts your spouse or common-law partner uses on their return

The form also lets employees claim:

  • Canada caregiver amounts for infirm children under age 18
  • Age amounts for employees 65 years or older
  • Disability amounts

The CRA also offers TD1-WS Worksheet for the Personal Tax Credits Return to help employees determine their appropriate age amount or Canada caregiver amount.

If you are in Québec, you have to fill both, the federal TD1X as well as the provincial Form TP-1015.R.13.1, Statement of Commissions and Expenses for Source Deduction Purposes. You may also visit the Revenu Québec's website to know more about Tax credits.

Payroll Tax: What Provincial or Territorial Tax Tables Should You Use?

As an employer, you must know each of your employees’ province or territory of employment so you can withhold the proper deductions when you file your payroll online. This depends on whether your employee physically reports for work at your establishment or place of business.

If your employee works from home, they might pay taxes to a different province or territory than your small business.

For income tax, Canada Pension Plan (CPP) or Québec Pension Plan (QPP) and Employment Insurance (EI) or Québec Paternal Insurance Plan (QPIP) withholding purposes, an “establishment of the employer” is any place or premises in Canada that you, as the employer, own, lease, or rent. It’s usually where one or more employees report to work or where one or more employees receive payment. This doesn’t have to be a permanent physical location.

For example, the place of business for a construction company can be one or more construction sites, or the place of business for a carnival can include a shopping mall parking lot. In these examples, the employee’s province or territory of employment is the location of the construction office or shopping centre parking lot.

If your employee reports to your establishment in person, the employee’s province or territory of employment is the same as that used for your office.

Example 1

Your head office is in Ontario, but you require your employee to report to your place of business in Manitoba. In this case, use the Manitoba payroll deductions tables.

Example 2

Your employee works from a home office in Alberta but occasionally has to report to your Alberta office. You pay your employee from your head office in Ontario. Here, you use the Alberta payroll deductions tables since the employee sometimes reports to your Alberta office.

If your employee doesn’t have to report to your establishment in person (for example, the employment contract says the employee works from a home office), the province or territory of employment is the region where your employee’s salary and wages are paid, usually the location of your payroll department or payroll records.

Example 3

Your employee doesn’t have to report to any of your places of business, but you pay the employee from your office in Québec. In this case, use the Québec payroll deductions tables. The employee doesn’t have to pay CPP contributions but may have to pay Québec Pension Plan (QPP) contributions.

For more details, visit Revenu Québec's sites on Québec Pension Plan (QPP) or Employment Insurance (EI) or Québec Paternal Insurance Plan (QPIP).

Calculating Deductions

Once you determine the province or territory to use for deducting CPP contributions, EI premiums, and income tax, you can use the payroll deductions online calculator to determine the employer share you need to deduct from each pay period. You also need your employee’s completed Personal Tax Credits form to finish calculating all the deductions you need to take from their pay.

Hold any of the deductions you take from an employee’s pay in trust for the receiver general in a separate account from your operating business account so that you have the funds readily available when it comes time to remit them to the CRA.

Remitting Payroll Tax Deductions on Time to Avoid Late Fees

As an employer, you need to remit the CPP or QPP contributions, EI or QPIP premiums, and income tax you deduct from your employees to the correct agency. For CPP or QPP and EI or QPIP, you also need to remit the employer’s portion to the CRA or RQ. Hefty penalties can occur if you’re late remitting your payroll deductions.

1) Determine Your Remittance Due Date

Identify the payday for your employee. This isn’t the pay period end date. It’s the day that your employees receive the funds from the previous pay period.

Example: The pay period is from July 3 through July 16, but you pay the employee on July 24. You use July 24 to calculate the remittance date.

If you are in Québec, visit Revenu Québec's website to view remittance schedules for your provincial deductions.

2) Calculate Your Average Monthly Withholding Amount (AMWA)

Use the AMWA calculation:

Total the following for the past two calendar years:

AMWA = (CPP + EI + income tax) / Number of months for which you’re required to make payments

Note: CPP and EI (Both the employee and employer portion)

Example for New Business:

You open your business on Jan 1, 2019, and hire your first employee on March 1, 2019. In June, you finally get the time to set up your payroll account with the CRA. You keep the CPP or QPP, EI, and income tax aside in a separate account for remittance to the correct agencies, since March 1, 2018.

You need to make payments for four months: March, April, May, and June. The amounts you set aside total $5,000.

AMWA = $5000/4

AMWA = $1250

Note: The pension calculations will vary if you are in Québec. Visit Revenu Québec's website for calculation of tax to be remitted.

3) Determine Your Remittance Type and Frequency Using the CRA Table

Use the CRA’s table of remitter types, average monthly withholding amounts, and due date. If you are in Québec, visit RQ's website to view frequency of remittances for your provincial deductions.

Note: If your due date is a Saturday, Sunday, or public holiday, your remittance is due on the next business day after holiday or weekend.

4) Complete the Remittance Forms

Depending on your remitter type, the CRA sends your small business a personalized form to fill out and set up the account. The CRA offers a variety of forms to make filing your taxes as a small business owner easier, whether it’s taxing employees’ pay or calculating sales taxes.

If you are in Québec, refer to the RQ website for the Remittance forms.

Late Remittance and Penalties

The CRA can apply a penalty if the following occur:

  • You deduct the amounts but don’t remit them to the CRA
  • You deduct the amounts but send the remittance late to the correct agency

These are the penalties:

  • 3% for amounts one to three days late 5% for amounts four or five days late 7% for amounts six or seven days late
  • 10% if the amount is more than seven days late or if you don’t remit any amount

When you set up your company’s payroll online, you need to make sure that you do it correctly the first time to ensure everyone gets paid on time and you avoid penalties. To ensure your payroll set goes smoothly consider adding a trusted payroll software like QuickBooks. Add online payroll today and streamline the payroll process.

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