Checking with the employee that the number is correct is the first step in these situations, so I'm glad to hear that you've already got that checked off the list. QuickBooks Online's Payroll systems are designed to recognize CRA assigned SIN numbers, whether they're for a permanent resident or something temporary granted to the individual. I'll point you in the right direction with getting this sorted out.
After verifying the number with the employee, the next step is to consider what kind of SIN number it is. Certain SIN numbers might be causing issues in the program, such as a temporary SIN that's expired. It's important to verify that that's not the case.
I encourage you to review these two CRA articles to find out what kind of SIN your employee has and then to get in touch with QuickBooks Online support for further assistance if needed.
Here's how you can contact support.
Phone and Chat: Click Contact Us to learn how to reach phone and chat support.
Schedule a Callback: click (?)Help in the upper right > click Contact Us > explain your situation > click Let's Talk > choose Get a callback (Note: Callback hours are the same as regular phone hours.)
Give us a shout and we'll get you back on track! Have a great week.