Classical eddy viscosity model deviates from the actual mean current profiles, when calculating the mean current profiles over rippled-beds in the presence of non-breaking waves, owing to the neglect of the enhancement of the wave boundary layer thickness by ripples and the wave-induced shear stress (the radiation stress and the wave Reynolds stress). Considering these shortcomings, a semi-empirical one-dimensional vertical (1DV) model is presented in this study. The present model was obtained using the two-dimensional Navier–Stokes equations and eddy viscosity assumptions, which differ from those of previous researchers, while a top-to-bottom sequence was adopted to calculate the mean current profiles. Empirical formulae were derived from the laboratory measurements and used in the present model to accurately predict the wave boundary layer thickness and bed roughness. The present model is in satisfactory agreement with the data from laboratory experiments. The factors influencing the mean current profiles were analyzed also. The wave-induced second-order shear stresses were found to be the principal reason for the deviations of the mean current profiles in the near-surface layer; as the influencing factors of wave-induced shear stress, the intensity of the wave relative to the current, the angle between the wave and current, and the size of ripples can also have a non-negligible effect on the mean current profiles.