ABSTRACTNanocomposites of polyetheretherketone (PEEK) and hydroxyapatite (HA) nanoparticles treated with a silane coupling agent were successfully prepared by twin screw extrusion and injection molding. Some of the samples were annealed after the injection molding. The silane treatment promoted an improvement of the short‐ and long‐term mechanical properties of the nanocomposites. A higher stress and a six times higher deformation at break and a higher impact strength were observed in the silane‐treated nanocomposites when compared to the nontreated ones. The number of cycles to fail of the treated nanocomposites was almost 200% higher than the number of cycles to fail of the nontreated samples. The treatment also decreased the glass transition temperature and amount of crystallinity of the samples. This improvement in mechanical properties obtained from the silane treatment was attributed to the strengthening of the PEEK/HA interfacial bond, to the plasticization of the PEEK matrix by silane oligomers produced during the processing and to a better dispersion of the HA nanoparticles within the PEEK matrix. Samples annealing, however, diminished all these properties due to the increase in crystallinity. Studies of the short‐ and long‐term mechanical properties of these nanocomposites under physiological conditions and of the proliferation of stem cells are under way. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 44476.