A method is for manufacturing a magnetoresistance effect element having a magnetization fixed layer, a non-magnetic intermediate layer, and a magnetization free layer being sequentially stacked. The method includes: forming at least a part of a magnetic layer that is to become either one of the magnetization fixed layer and the magnetization free layer; forming a function layer including at least one of an oxide, a nitride, and a fluoride on the part of the magnetic layer; and removing a part of the function layer by exposing the function layer to either one of an ion beam and plasma irradiation.