Annealing plays an important role in modifying structures and properties of ferromagnetic shape memory alloys (FSMAs). The annealing effect on the structures and magnetic properties of off-stoichiometric Fe₄₅Mn₂₆Ga₂₉ FSMA has been investigated at different elevated temperatures. Rietveld refinements of neutron diffraction patterns display that the formation of the ɣ phase in Fe₄₅Mn₂₆Ga₂₉ annealed at 1073 K increases the martensitic transformation temperature and reduces the thermal hysteresis in comparison to the homogenized sample. The phase segregation of a Fe-rich cubic phase and a Ga-rich cubic phase occurs at the annealing temperature of 773 K. The atomic occupancies of the alloys are determined thanks to the neutron's capability of differentiating transition metals. The annealing effects at different temperatures introduce a different magnetic characteristic that is associated with distinctive structural changes in the crystal.