Compare origination and underwriting fees along with closing costs. If you’re getting an SBA loan, expect an SBA loan guarantee fee. The lender pays this fee and has the option to pass it along to you at closing. Note that lenders can’t charge a separate origination fee on an SBA 7(a) loan, though they can charge packaging fees that are reasonable and customary for the services performed. Other fees associated with a small-business loan include late payment fees, check processing fees and prepayment fees, which are charged if you make early payments.