Fused deposition modeling (FDM) is a rapidly growing three-dimensional (3D) printing technology and has great potential in medicine. Polyether-ether-ketone (PEEK) is a biocompatible high-performance polymer, which is suitable to be used as an orthopedic/dental implant material. However, the mechanical properties and biocompatibility of FDM-printed PEEK and its composites are still not clear. In this study, FDM-printed pure PEEK and carbon fiber reinforced PEEK (CFR-PEEK) composite were successfully fabricated by FDM and characterized by mechanical tests. Moreover, the sample surfaces were modified with polishing and sandblasting methods to analyze the influence of surface roughness and topography on general biocompatibility (cytotoxicity) and cell adhesion. The results indicated that the printed CFR-PEEK samples had significantly higher general mechanical strengths than the printed pure PEEK (even though there was no statistical difference in compressive strength). Both PEEK and CFR-PEEK materials showed good biocompatibility with and without surface modification. Cell densities on the “as-printed„ PEEK and the CFR-PEEK sample surfaces were significantly higher than on the corresponding polished and sandblasted samples. Therefore, the FDM-printed CFR-PEEK composite with proper mechanical strengths has potential as a biomaterial for bone grafting and tissue engineering applications.