If you take out an SBA 504 Loan for 20 years or 25 years, you have to pay back the money for 10 years before you can do it. In the same way, there is a five-year prepayment penalty for SBA loans with a 10-year term. To pay off your loan in the 9th year, you'll pay 20% of 3%, which comes out to 0.6%.