If I created my Repl.it account with an email.
But I applied to the Github Student’s Plan with my school email and got accepted.
How would I be able to link my Repl.it account to the Github one, even though it’s two different emails.
It’s not like I can sign in to my Repl.it account using the Github one. 
Go to this page then scroll all the way down and connect your Github account. I don’t think there should be a problem even with the 2 different emails.
It didn’t work. I now have a new account with hacker.
Another solution would have been to edit your profile and change your associated email address to your school email. Did you try this?