There is increasing interest in the use of polyether ether ketone (PEEK) for orthopedic and dental implant applications due to its elastic modulus (close to that of bone), biocompatibility and radiolucent properties. However, PEEK is still categorized as bioinert owing to its low integration with surrounding tissues. Methods such as depositing hydroxyapatite (HA) onto the PEEK surface could increase its bioactivity. However, depositing HA without damaging the PEEK substrate is still required further investigation. Friction stir processing is a solid-state processing method that is widely used for composite substrate fabrication. In this study, a pinless tool was used to fabricate a HA/PEEK surface nanocomposite for orthopedic and dental applications. Microscopical images of the modified substrate confirmed homogenous distribution of the HA on the surface of the PEEK. The resultant HA/PEEK surface nanocomposites demonstrated improved surface hydrophilicity coupled with better apatite formation capacity (as shown in the simulated body fluid) in comparison to the pristine PEEK, making the newly developed material more suitable for biomedical application. This surface deposition method that is carried out at low temperature would not damage the PEEK substrate and thus could be a good alternative for existing commercial methods for PEEK surface modification.