Microstructure and mechanical properties in friction stir processed (FSPed) Zr-based bulk metallic glass were investigated. The microstructure in the friction zone (FZ) exhibits an amorphous “band-like” structure with a small number of nanoscale crystalline particles. On the other hand, the microstructure in the FZ near the finish point of the process exhibits a large number of nanocrystalline particles in size of less than 20nm and amorphous phase. The difference of the microstructure in each FSP region is explained from the difference of the heat input by FSP. The hardness in each FSPed region shows higher value compared with that of other Zr-based balk metallic glasses with almost the same volume fraction of crystalline phase.