How Much a Loan Origination Fee Costs. The average loan origination fee is 1 percent of your mortgage. That means a $150,000 mortgage will cost about $1,500 in loan origination fees and a $500,000 mortgage will run you in the neighborhood of a $5,000 loan origination fee. Your mortgage might also have an underwriting fee, which some lenders charge for researching whether to approve you for the loan.