Many businesses treat the filing of a return as the finish line. 

It is not. 

Filing a return and paying a balance owing are two separate obligations. The return reports what is owed. The payment satisfies it. Treating them as the same thing is one of the most common, and most avoidable, causes of interest charges, misapplied payments, and unnecessary friction with the Canada Revenue Agency (CRA). 

For any business working with an accounting and bookkeeping firm in Toronto or across Canada, knowing how to pay the CRA correctly is part of disciplined financial management. Whether the balance relates to corporate income tax (T2), GST/HST, or payroll remittances, the payment must reach the correct program account, on time, and through an approved method. 

This guide explains the most common ways to remit a balance to the CRA, the information to have ready before paying, and the mistakes that cost businesses both time and money. 

Filing and Paying Are Two Separate Obligations  

A corporation can file a flawless return and still fall offside if the payment is late, incomplete, or applied to the wrong account. 

Filing deadlines and payment deadlines are not always the same. For many corporations, the balance of tax is due before the return itself. Interest begins to accrue on any unpaid balance from the due date, regardless of when the return is filed. 

This is why payment should be treated as a scheduled event, not an afterthought. A business that knows what it owes, which account it belongs to, and how it will pay is far less exposed than one that scrambles at the deadline. 

What You Need Before You Pay 

Before making any payment to the CRA, have the following ready: 

• Business Number (BN): a nine digit number followed by a program identifier 

• The correct program account, which tells the CRA what the payment is for: 

• RC (for example, RC0001) for corporate income tax 

• RT (for example, RT0001) for GST/HST 

• RP (for example, RP0001) for payroll deductions 

• The relevant tax year-end or reporting period 

• The exact amount owing 

The program identifier matters. A payment entered against the wrong account, such as corporate tax instead of payroll, can create a balance in one account and an apparent shortfall in another, even though the money was paid. 

Important: Any payment to the Receiver General over $10,000 must be made by electronic means. Cheques are still accepted for amounts of $10,000 or less, but electronic payment is strongly recommended for speed, security, and traceability. 

The Most Common Ways to Pay the CRA 

There are several approved ways to remit a balance to the CRA. The right one depends on the amount, the timing, and the account being paid. 

1. Online Banking (Recommended) Online banking is the fastest and most reliable method for most businesses. 

Log in to your business online banking with any major Canadian financial institution, select Add Payee, and search for the correct CRA payee name. Common options include: 

• Federal Corporation Tax Payments (often shown as TXINS) for T2 balances and instalments 

• Federal GST/HST Payment (often shown as GST-P) for GST/HST 

• Federal Payroll Deductions (often shown as EMPTX or PD7A) for payroll Enter your fifteen character account number, for example 123456789RC0001, add the amount, and submit. Save the confirmation number and a screenshot for your corporate records. Once a payee is set up, future instalments and balances can be paid in under a minute. 

2. CRA My Payment 

CRA My Payment lets you pay using Visa Debit, Debit Mastercard, or Interac Online from a 

participating Canadian financial institution. Credit cards are not accepted through this service. 

On the CRA website, select Pay now, choose Businesses, select the relevant program such as corporate income tax (T2), enter the BN, tax year, and amount, then complete the payment. It is immediate and provides instant confirmation. 

3. Pre-Authorized Debit (PAD) 

A pre-authorized debit is set up through CRA My Business Account. Select the relevant account, choose Proceed to pay, then Pre-authorized debit, and follow the prompts to schedule a one time or recurring payment. 

PAD takes about five business days to set up the first time, so it should be arranged in advance rather than at the deadline. It is well suited to recurring obligations such as payroll remittances and tax instalments. 

4. Wire Transfer 

Wire transfers are typically used by non-resident corporations or for very large payments. The banking details and SWIFT code are available on the CRA website. The BN and program identifier must always be included as a reference, otherwise the CRA may be unable to apply the payment correctly. 

5. In Person at a Canadian Financial Institution 

Payments can be made in person at your bank using the personalized remittance voucher provided by the CRA. If you do not have a remittance voucher, one can be requested through CRA My Business Account, or your accounting firm can obtain it on your behalf. 

6. By Cheque (only if the balance is $10,000 or less) 

Make the cheque payable to the Receiver General for Canada, and write the BN and tax year-end on the front, for example 123456789RC0001, T2 year-end 2025-12-31. Mail it with the remittance voucher to the CRA. 

Keep in mind that the CRA considers a payment received on the date it actually reaches the CRA or its agent, not the date it was mailed. Allow at least five business days for delivery. 

Why Payment Timing Matters 

The date a payment is received, not the date it is sent, is the date that counts. 

This single detail causes more avoidable interest charges than almost any other. A cheque mailed on the deadline is late. A pre-authorized debit arranged the day before a deadline may not be active in time. Electronic payments made through online banking or CRA My Payment are the safest way to ensure the CRA receives funds on the intended date. 

For businesses managing multiple obligations across corporate tax, GST/HST, and payroll, a clear payment calendar is essential. 

Common CRA Payment Mistakes Businesses Make  

Across small and mid-sized businesses, the same payment mistakes appear repeatedly: 

• Paying the wrong program account, so the money sits against corporate tax instead of payroll, or the reverse 

• Missing the electronic payment threshold by issuing a cheque for an amount over $10,000 

• Assuming the mailing date is the payment date, which leads to late charges 

• Not keeping the confirmation number, which makes payment difficult to prove if a balance is later questioned 

• Treating payment as an afterthought rather than part of a structured compliance calendar 

None of these mistakes are complicated. They simply reflect the difference between a business that has a system and one that does not. 

How Payment Fits Into a Stronger Compliance System  

Paying the CRA is not a standalone task. It is the final step in a chain that begins with accurate bookkeeping. 

When books are current, balances are known well before deadlines. When GST/HST and payroll are tracked monthly, there are no remittance surprises. When records are clean, the correct amount is paid to the correct account the first time. 

In other words, how well a business pays the CRA is a direct reflection of how well its records are maintained throughout the year. Strong bookkeeping and accounting services in Toronto should connect record keeping, reporting, and payment into a single, predictable process. 

The Progress Group Approach 

At Progress Group, our Toronto accounting and bookkeeping services are built to support the full compliance cycle, not just the filing of a return. 

We help businesses: 

• Prepare and file corporate tax (T2), GST/HST, and payroll obligations 

• Know what is owed, and to which CRA program account, well before deadlines 

• Set up and manage CRA payment methods, including online banking and pre-authorized debit 

• Maintain a clear filing and payment calendar across all accounts 

• Keep clean, tax-ready records that support every payment made 

• Respond quickly and confidently to any CRA review 

Our work is designed to help businesses move from reactive filing to structured tax management. 

Because paying the CRA should never be guesswork. It should be built into the way the business operates.