The effects of the fatigue deformation on the localized deformation of a ZCAP-3 bulk metallic glass (BMG) were studied using the nanoindentation technique. A localized mechanical hardening was observed in the ZCAP-3 BMG between the shear bands in the fatigue-damaged zone. In contrast to the indentations of the BMG made far away from the fatigue-damaged zone, there was no indentation size effect. Both the reduced contact modulus and the indentation hardness were larger than those corresponding to the indentations of the ZCAP-3 BMG in the undamaged zone. These observations revealed the possible effects of local heating and stress-induced atomic rearrangements (i.e., inelastic deformation) on the reduction of the free volume in the BMG from the propagation of the fatigue crack.