How Mortgages Work. The origination fee is how lenders make money up front on your mortgage loan. Origination fees are calculated as a percentage of the total loan, usually between 0.5 and 1 percent on U.S. mortgages [source: Investopedia]. Going back to our APR example, let's say that the second lender charges a 3 percent origination fee, plus an application fee and other costs totaling $3,820 at closing.