Hydrogen Embrittlement (HE) leads to deterioration of the fracto-mechanical properties of metals. In spite of vast literature, it is still not clearly understood and demands significant research on this topic. For better understanding of the hydrogen effect on fatigue behaviour of metals, present work focuses on developing a computational framework for fatigue crack initiation studies in metals in the presence of hydrogen. The developed framework consists of a nonlocal crystal plasticity model coupled with hydrogen transport model to study the fatigue behaviour of hydrogen charged metals. The nonlocal crystal plasticity model accounts for the statistically stored dislocations (SSDs) and geometrically necessary dislocations (GNDs) in polycrytalline metal. Hydrogen transport model, on the other hand, accounts for diffusion and trapping behavior of hydrogen due to concentration gradient, pressure gradient, plastic strain-rate with dislocations as the only trapping sites along the slip systems. A polycrystalline representative volume element (RVE) with periodic boundary conditions is used in this study. Fatigue crack initiation criterion is proposed for the simulated RVE with controlled microstructure by considering a critical value of the fatigue indicator parameter (FIP). FIP is formulated based on the experimental observations of several crack initiation sites along the grain boundaries, their normal direction with respect to loading direction and the accumulated plastic strain in nickel polycrystalline samples. Developed simulation framework correctly accounts cyclic stress-strain behavior and multiple fatigue crack initiation sites observed experimentally in the presence of hydrogen.