Having student loan debt will affect your credit score, but not always in the way you think. If you consistently make on-time student loan payments, your student loans can boost your credit score. But if you pay late, or default, on student loans, your credit score will take a hit.ow Defaulting on a Student Loan Affects Your Credit Score. If you stop making payments (default) on your student loan, your credit score will go down. Late student loan payments will hurt your score in much the same way as late payments on any other type of account.