We examined the diffusion of hydrogen atoms in mono-, bi- and tetralayer graphene with AB stacking and two bilayer graphene with stacking faults using density functional theory. The bi- and tetralayer graphene provide diffusion pathways with lower energy barriers inside the interlayer space. Inside the bi- and tetralayer graphene with AB stacking, the in-plane diffusion is more favorable than the inter-plane jumping. However, the stacking faults made by sliding layer planes lowers the energy barrier of the inter-plane jumping and the effective frequency of the inter-plane jump is larger than that of the in-plane diffusion inside the graphene layers with the stacking faults. This suggests that hydrogen atoms can diffuse over a long distance inside few-layered graphene with stacking faults jumping consecutively between adjacent layers.