Yes SBA 7(a) and 504 loans have prepayment penalties. For 7(a) loans, the fees only apply to loans with terms exceeding 15 years, and only if you pay more than 25% of your balance in the first year. On the other hand, 504 loans have prepayment penalties that decrease during the first 10 years of the loan, reaching 0% at the halfway point in your loan term.