How to Pay HST Online in Canada: Step-by-Step Guide

Paying Harmonized Sales Tax (HST) online means remitting the GST/HST you collected (or owe) to the Canada Revenue Agency (CRA) electronically. 

If you are a small business owner in Canada with an HST balance owing (or an instalment reminder), this guide will walk you through a fast and error-free HST online payment process. You’ll learn which method is right for your situation, what to prepare before you pay, and what to do if something goes wrong.

Here at Premium Bookkeeping & Accounting, GST/HST compliance is one of the most common areas where we help Canadian small businesses avoid costly CRA notices — usually because of a misapplied payment or a missed deadline. This guide gives you the same process we use with our clients.

Confirm Your Payment Type Before You Pay

CRA applies payments differently depending on what you’re paying. If you choose the wrong payment type, your payment can be delayed, misapplied, or show up in the wrong place.

Pre-Payment Checklist

Before you pay, have these ready:

• Your Business Number (BN) and GST/HST program account (example format: 123456789RT0001)
• The amount you’re paying
• The reporting period (if applicable)
• Your CRA login (if using CRA portals)
• Your bank login (if using online banking bill payment)
• A debit card that works online (if using CRA My Payment)
• A folder to save your confirmation (digital or printed)
• 5 minutes to double-check your payee name and reference number — this single step prevents most payment errors.

If you’re unsure whether you’re paying an instalment or a return balance, check My Business Account or call the CRA.

Choose the Best Online Payment Method

There are three main ways to pay HST online in Canada. The “best” method depends on how quickly you need confirmation and what access you have.

Which HST Online Payment Method Is Right for You?

Our Recommendation:

• Online banking bill payment — best for most businesses that already pay bills online.
• CRA My Payment — best if you want an immediate debit-card payment and quick proof.
• Pre-authorized debit (PAD) — best if you want to schedule payments ahead of time.

TIP: Processing speed varies by bank — some post payments faster than others. If you’re close to a deadline, pay 1–2 business days early to be safe.

Method 1 — How to Pay HST Online via Online Banking (Bill Payment)

This is the most common way business owners make an HST payment online. The key is selecting the correct CRA payee and entering the full reference number.

Step-by-Step Instructions (Online Banking)

1. 1. Sign in to your bank’s online or mobile banking. Use your business account for GST/HST payments. Some personal banking profiles don’t show the full CRA payee list.
   2. Go to Bill Payments → Add a Payee. Every bank labels this slightly differently, but you’re looking for “Pay Bills” and then “Add Payee.”
      
   3. Search for the correct CRA payee (GST/HST-specific). This is where many payments go wrong. Look for a payee that clearly references GST/HST.
      
      Common payee names vary by bank — the exact wording won’t be identical everywhere. Look for options that clearly reference GST/HST, such as: 
      • Federal – GST/HST Payment (often used for remittances/balance owing) 
      • Federal – GST/HST Return and Payment (used when paying with/for a filed return)

Your bank may label these slightly differently. If you’re not sure which to choose, log into My Business Account to confirm your account type before paying.

1. Enter your reference number (your GST/HST account). This is usually your 15-character BN + program account, like: 123456789RT0001
2. Enter the payment amount. Double-check the amount matches your scenario (balance owing vs instalment vs arrears).
3. Choose the payment date. If you’re close to the due date, schedule for the earliest possible date. Banks have cutoffs. Paying late in the day can push processing to the next business day.
4. Submit the payment. Review everything one last time: payee name, reference number, and amount.
5. Save proof immediately. Screenshot or download the confirmation page and store it in your “CRA Payments” folder.

Payee Name & Reference Number Tips (Do/Don’t)

• Always use the GST/HST-specific payee, not a general CRA option.
• Double-check all 15 characters—missing one digit can delay the application.
• Have multiple RT (Registration Type) accounts (e.g., payroll, GST/HST)? Confirm you’re using the correct one.

Confirmation & Recordkeeping Checklist

Keep proof of every payment. Here’s the checklist:

• Save/screenshot confirmation number
• Note date, amount, method, and reporting period in bookkeeping software
• File proof in a “CRA Payments” folder
• Reconcile the payment against your HST payable account within 3 business days

Method 2 — Pay HST via CRA My Payment (Debit Card)

CRA My Payment is a CRA portal that lets you pay using an eligible debit card online. It’s great when you want quick confirmation without setting up a bank bill payee.

Step-by-Step Instructions (CRA My Payment)

1. Go to the CRA My Payment page on Canada.ca (search “CRA My Payment”).
2. Select Pay now and choose GST/HST as the payment type.
3. Enter your Business Number and program account (example: 123456789RT0001).
4. Enter the payment amount (and reporting period if prompted).
5. Choose your card type and complete the payment using Visa Debit or Debit Mastercard.
6. Review the summary, confirm, and save/print the confirmation page.

What to Watch For (Limits and Common Errors)

• Debit cards only — CRA My Payment does not accept credit cards.
• Daily limits apply — many banks cap daily debit transactions (often $3,000–$5,000).
• No scheduling — CRA My Payment is immediate; use PAD for future-dating
• Wrong category = misapplied payment — if you choose the wrong payment type (like corporate tax), your payment can land in the wrong place.

TIP: If you’re hitting bank limits, you can sometimes split the payment into two transactions or request a temporary limit increase from your bank before you pay.

Method 3 — Pay HST via Pre-Authorized Debit (PAD)

PAD is best when you want to schedule a payment in advance (especially for instalments) or set up a recurring pattern.

Step-by-Step Instructions (PAD)

1. Sign in to CRA My Business Account (learn how to set up your CRA My Business account here).
2. Navigate to the Make a Payment option. The label may vary slightly depending on your account view.
3. Choose Pre-authorized debit (PAD) and select one-time or recurring.
4. Enter your chequing account details (transit number, institution number, account number).
5. Set the payment date and amount (and frequency if recurring).
6. Review terms, submit, and save the confirmation page.
7. CRA will send a confirmation to your CRA My Business Account online mail — check it within 1–2 business days.

At Premium Bookkeeping & Accounting, PAD is popular for recurring clients because it reduces missed payments and saves administrative time each quarter. If managing quarterly remittances feels like one more thing on your plate, our Tax Preparation service handles the whole process for you.

Timing Rules You Must Know (PAD)

• Schedule PAD at least 5 business days before the due date.
• Avoid weekends/holidays (withdrawals process on business days).
• If a due date falls on a weekend/holiday, CRA generally accepts payment on the next business day—but schedule early to be safe.

When to Pay HST Online (Before or After Filing?)

Canadian small businesses often wonder whether to pay HST online before or after filing. Here’s what we recommend.

Common HST Online Payment Mistakes & How to Avoid Them

Why Do HST Payments Get Misapplied?

These are the top failure points that cause misapplied payments and CRA notices.

#1) Process gap: Picking the wrong CRA payee in online banking

System fix: Choose a GST/HST-specific payee (not a generic CRA). Verify before submitting.

#2) Process gap: Entering an incomplete reference number

System fix: Use the full BN + RT account (15 characters). Copy it from CRA correspondence or My Business Account.

#3) Process gap: Paying the right amount to the wrong payment type (instalment vs balance owing)

System fix: Use the scenario table above. If it’s wrong, you may need CRA to reallocate.

#4) Process gap: Paying on the due date after your bank cutoff

System fix: Pay 1–2 business days early. Confirm your bank’s cutoff time.

#5) Process gap: Not saving proof of payment

System fix: Screenshot confirmation immediately and store it the same day.

Best practice: At Premium Bookkeeping & Accounting, we have a rule of thumb and that’s: always pay 2 days early! This prevents most late-payment notices.

What to do if Your Online HST Payment Isn’t Showing?

#1) Check When You Paid

Weekend and holiday payments don’t process until the next business day. If you paid Friday evening, it may not post until Monday.

#2) Verify your confirmation details

✓ Payee name correct?

✓ Reference number correct (full BN + RT account, e.g. 123456789RT0001)?

✓ Amount correct?

#3) Wait out the full processing window

Don’t escalate until the full window has passed unless you’re close to a deadline.

#4) If it’s still missing, escalate

Still missing after the full processing window? Here’s what to do.

Have this ready before you call:

• confirmation number
• payment date
• amount
• payee selected
• BN/RT account number

Who to contact:

• Bank bill payment — contact your bank first to confirm the payment was sent and the date it was processed.
• Then contact CRA Business Enquiries with your confirmation details.

Ready to Stop Managing HST on Your Own?

You now have everything you need to pay HST online in Canada without a misapplied payment or a CRA notice. Pick your method, follow the steps, save your confirmation, and pay early.

That said, paying HST is only one part of staying compliant — and misapplied payments, missed deadlines, and incorrect return amounts are exactly where the risk compounds. 

At Premium Bookkeeping & Accounting, we’ve built systems around GST/HST compliance so our clients don’t have to think about it. If you’d rather have a process that runs without you, our bookkeeping services are built around exactly that kind of ongoing compliance work.

Want to talk through your GST/HST setup? Get in touch with our team.

Further Reading

If this guide was useful, these resources cover the full GST/HST picture:

→ What Is Harmonized Sales Tax (HST)? An Updated 2026 Guide for Canadian Small Businesses — the foundational guide on how HST works, who it applies to, and how rates vary by province.

→ CRA My Business Account: Your Complete Guide to the Portal That Simplifies Business Taxes — how to set up and navigate the portal you’ll use for PAD payments, account balances, and CRA correspondence.

→ GST/HST Guide for Canadian Businesses: Rules, Thresholds & Filing Mistakes (2026) — the complete overview of GST/HST rules, registration thresholds, ITCs, place-of-supply, and the costliest filing mistakes to avoid.

→ Corporate Year-End in Canada: Step-by-Step Checklist for Small Business Owners — HST reconciliation is part of a clean year-end. This checklist covers everything you need to close the books properly.