There have been numerous efforts to understand and control the resistance of materials to fracture by repeated or cyclic stresses. The micromechanical behaviours, particularly the distributions of stresses on the scale of grain size during or after mechanical or electrical fatigue, are crucial to a full understanding of the damage mechanisms in these materials. Whether a large microstress develops during cyclic deformation with a small amount of monotonic strain but a large amount of accumulated strain remains an open question. Here, we report a neutron diffraction investigation of the development of intergranular stresses, which vary as a function of grain orientations, in 316 stainless steel during high-cycle fatigue. We found that a large intergranular stress developed before cracks started to appear. With further increase of fatigue cycles, the intergranular stress decreased, while the elastic intragranular stored energy continued to grow: One implication of our findings is that the ratio between the intergranular and intragranular stored energies during various stages of fatigue deformation may validate the damage mechanism and can be used as a fingerprint for monitoring the state of fatigue damage in materials.