The synthesis and crystallographic site occupancy were investigated for MgAl2O4 with and without mechanical activation of the precursor powders. Heating to 1200 °C or higher resulted in the formation of a single spinel phase regardless of whether the powders were mechanically activated or not. Neutron diffraction analysis was used to determine cation site occupancy and revealed that mechanical activation resulted in a lower degree of cation site inversion compared to the nonactivated materials, which indicated that the powders were closer to thermodynamic equilibrium. This is the first study to characterize the effects of mechanical activation on crystallographic site occupancy in magnesium aluminate spinel using neutron diffraction.