The purpose of this study was to evaluate the influence of various polishing protocols on the surface roughness of polyetheretherketone (PEEK) and identify an effective polishing method of dental prostheses at the chairside. The PEEK specimens were assigned to seven groups with different protocols: no additional polishing (NT); polishing using a rubber point (C); polishing using “silky shine” (S); polishing using “aqua blue paste” (A); protocol C followed by protocol S (CS); protocol C followed by protocol A (CA); and protocol C followed by protocols S and A (CSA). The surface roughness (Sa and Ra) of the polished surfaces was measured. The surface roughness decreased in the following order of groups: NT, C, S, CS, CSA, CA, and A. In Groups C and S, wide deep pits formed by abrasive grains of SiC paper were observed, whereas only fine linear structures were observed on the surface in other groups. With respect to the polishing protocol of PEEK, clinically acceptable surface roughness was obtained using a soft polishing brush and agent for more than 3 min.