The hydrodynamic influence of surface texture on static surfaces ranges from large drag penalties (roughness) to potential performance benefits (shark-like skin). Although it is of wide-ranging research interest, the impact of roughness on flapping systems has received limited attention. In this work, we explore the effect of roughness on the unsteady performance of a harmonically pitching foil through experiments using foils with different surface roughness, at a fixed Strouhal number and within the Reynolds number range of. The foils' surface roughness is altered by changing the distribution of spherical-cap-shaped elements over the propulsor area. We find that the addition of surface roughness does not improve the performance compared with a smooth surface over the range considered. The analysis of the flow fields shows near-identical wakes regardless of the foil's surface roughness. The performance reduction mainly occurs due to an increase in profile drag. However, we find that the drag penalty due to roughness is reduced from for a static foil to for a flapping foil at the same mean angle of attack, with the strongest decrease measured at the highest. Our findings highlight that the effect of roughness on dynamic systems is very different than that on static systems; thereby, it cannot be estimated by only using information obtained from static cases. This also indicates that the performance of unsteady, flapping systems is more robust to the changes in surface roughness.