The role of hydrogen on intergranular (IG) fracture in hydrogen-assisted fatigue crack growth (HAFCG) of a pure iron at low stress intensity was discussed in terms of the microscopic deformation structures near crack propagation paths. The main cause of IG fracture was assumed to be the hydrogen-enhanced dislocation structure evolution and subsequent microvoids formation along the grain boundaries. Additionally, the impact of such IG cracking on the macroscopic FCG rate was evaluated according to the dependency of IG fracture propensity on the hydrogen gas pressure. It was first demonstrated that the increased hydrogen pressure results in the larger area fraction of IG and corresponding faster FCG rate. Moreover, gaseous hydrogen environment also had a positive influence on the FCG rate due to the absence of oxygen and water vapor. The macroscopic crack propagation rate was controlled by the competition process of said positive and negative effects.