The penetration of atomic hydrogen through defect-free graphene was generally predicted to have a barrier of at least several eV, which is much higher than the 1-eV barrier measured for hydrogen-gas permeation through pristine graphene membranes. Herein, our density functional theory calculations show that ripples, which are ubiquitous in atomically thin crystals and mostly overlooked in the previous simulations, can significantly reduce the barriers for all steps constituting the mechanism of hydrogen-gas permeation through graphene membranes, including dissociation of hydrogen molecules, reconstruction of the dissociated hydrogen atoms and their flipping across graphene. Especially, the flipping barrier of hydrogen atoms from a cluster configuration is found to decrease rapidly down to < 1 eV with increasing ripples’ curvature. The estimated hydrogen permeation rates by fully considering the distribution of ripples with all realistic curvatures and the major reaction steps that occurred on them are quite close to the experimental measurements. Our work provides insights into the fundamental understanding of hydrogen-gas permeation through graphene membranes and emphasizes the importance of nanoscale nonflatness (ripples) in explaining many surface and transport phenomena (for example, functionalization, corrosion and separation) in graphene and other two-dimensional materials