We investigated the effect of helium atmospheric-pressure plasma (PL) and deep-ultraviolet (UV) light treatments on the adhesive properties of fiber-reinforced poly(ether-ether-ketone) polymer (PEEK). PEEK disks reinforced with carbon (CPEEK) or glass (GPEEK) fibers were polished, modified with PL and UV for 60 s, and the surface energy was calculated by measuring the contact angles. The disk surfaces were analyzed by X-ray photoemission spectroscopy. Shear bond strength testing was performed using a universal testing machine, and the fracture surfaces were observed by electron probe microanalyzer. Data were analyzed with one and two-way ANOVA and Tukey’s post-hoc test (p < 0.05). The surface energies were increased by the modifications, which created OH functional groups on the surfaces. The bond strengths of CPEEK were increased by PL, and those of GPEEK were increased by PL and UV, owing to chemical bonding at the interface.