The fluid flow in a single rock fracture during shear processes has been an important issue in rock mechanics and is investigated in this study using the Finite Element Method (FEM), considering evolutions of aperture and transmissivity with shear displacement histories under different normal loading conditions. The distributions of fracture aperture and its evolution during shear were calculated from the initial aperture, based on the laser-scanned sample surface roughness features, and shear dilations measured in the laboratory coupled shear-flow tests. Three rock fractures with different roughness were used as parent samples from which nine replicas were made and tested under three normal loading conditions. For flow simulations, a special algorithm for treating the contact areas as zero-aperture elements was used to produce more accurate flow field simulations, which provide good agreement with the flow rate data obtained from the laboratory tests, showing that complex histories of fracture aperture and tortuous flow fields with changing normal stress and increasing shear displacements.