Using molecular dynamics simulations, the mechanical response of amorphous geopolymer binder (GB) under spherical nanoindentation was examined as a function of GB composition (Si/Al ratio), indenter size (radius of indenter) and loading rates. The observed hardness values were strongly dependent on the indenter size and loading rates. Specifically, the GB hardness increased with decreasing indenter size and increasing loading-rate. The indenter size effect and the effect of loading rate were related to the ease of rotation of the underlying Si and Al tetrahedra in conjunction with the breaking of bridging SiO and AlO bonds. Further, for a given indenter size, increasing the Si/Al ratio increased the hardness and Young’s modulus of the GB, which was correlated to higher strength of SiO bonds as compared to AlO bonds present in the GB.