Pump as turbine (PAT) is a factual alternative for electricity generation in rural and remote areas where insufficient or inconsistent water flows pose a threat to local energy demand satisfaction. Recent studies on PAT hydrodynamics have shown that its continuous operations lead to a progressive deterioration of inner surface smoothness, serving the source of near-wall turbulence build-up, which itself depends on the level of roughness. The associated boundary layer flow incites significant friction losses that eventually deteriorate the performance. In order to study the influence of wall roughness on PAT hydraulic performance under different working conditions, CFD simulation of the water flow through an axial-flow PAT has been performed with a RNG k-ε turbulence model. Study results have shown that wall roughness gradually decreases PAT’s head, efficiency, and shaft power. Nevertheless, the least wall roughness effect on PAT hydraulic performance was experienced under best efficiency point conditions. Wall roughness increase resulted in the decrease of axial velocity distribution uniformity and the increase of velocity-weighted average swirl angle. This led to a disorderly distribution of streamlines and backflow zones formation at the conduit outlet. Furthermore, the wall roughness impact on energy losses is due to the static pressure drop on the blade pressure surface and the increase of turbulent kinetic energy near the blade. Further studies on the roughness influence over wider range of PAT operating conditions are recommended, as they will lead to quicker equipment refurbishment.