During my university days, I use to take student loans. After few years, I realized that the loan has late payment fee. I have repented ever since. But now the money sits on my account, what can I do? Can I use it?

If you are able not to fall into the riba otself then that takes priority, otherwise you will get in trouble if you don't pay the debt, and Allah knows best. You have to give me mote details so I know as this is just a general pointer.