The results obtained from the self-propulsion simulations using Computational Fluid Dynamics (CFD) in the current study, for a ship free to heave, pitch and surge with the means of a weak spring system, are combined with the formerly executed CFD results of the bare hull and propeller open water simulations to investigate the impacts of regular head waves on the propeller-hull interactions in comparison to calm water, at the self-propulsion point of the model. Despite a rather significant dependency of the nominal wake on the wave conditions, the Taylor wake fraction remains almost unchanged in different studied waves which is around 12% lower than the calm water value. The thrust deduction factor in waves is reduced (12.8%–26.1%) in comparison to the calm water value. The change of thrust deduction factor is found to be associated with the boundary layer contraction/expansion and vortical structure dynamics, originating from the wave orbital velocities as well as the significant shaft vertical motions and accelerations that resulted in a modified propeller action, and consequently diminished suction effect on the aft ship. The altered thrust deduction factor and wake fraction in waves in comparison to calm water underlines the significance of waves on the propulsive factors and propeller design.