Nucleation of shear bands is of critical importance in the deformation behaviors of metallic glasses, but the detailed examination of nucleation kinetics and the correlation with the structure and relaxation kinetics has been few. Here, based upon instrumented nanoindentation with spherical indenter and a great deal of the observed first pop-in events, one unique trimodal distribution of shear band nucleation events in a Gd-based metallic glass was reported. Four different loading rates were employed to study the evolution of the nucleation distribution with external loading. In the analyses of nucleation kinetics, the site density, nucleation rate and activation barrier for three nucleation events were obtained based on the cooperative deformation model, which clearly display the trimodal character. The discovery of a trimodal shear band nucleation distribution provides new insights for understanding the relationship between the heterogeneous structure, relaxation kinetics and deformation mechanism and opportunities for controlling the ductility of amorphous alloys. •An effective strategy by nanoindentation reveal the multiple distribution of shear band nucleation.•A unique trimodal distribution of shear band nucleation sites in Gd-based MG for the first time.•The diagram of first pop-in load with loading rates for three nucleation sites were plotted.•The nucleation sits density, nucleation rate and activation barrier for three nucleation sites were determined.•The types of shear band nucleation sites are related to the types of characteristic relaxation behavior.