Ribosomal protein S3 (rpS3) has endonuclease activity for DNA repair. In particular, rpS3 cleaves the phosphodiester bonds of damaged DNA. In this study, we show that the repair domain of rpS3 spans amino acids 144-189. We fused rpS3 with the transactivator of transcription (TAT) sequence to introduce the rpS3 repair domain into cells. We find that the TAT-rpS3 (aa: 144-189) peptide cleaves UV-induced cyclobutane pyrimidine dimers (CPDs) in cells. We also reveal that the TAT-rpS3 peptide reduces matrix metalloproteinase-1 (MMP-1) induction in UV-irradiated fibroblasts and increases cell migration activity. Taken together, our study suggests that penetration of the rpS3 repair domain into cells can cleave UV-induced CPDs and reduce MMP-1 expression induced by UV.