This study examines the effect of functionalized multi‐walled carbon nanotube (CNTs) dispersion on mechanical properties of poly‐ether‐ether‐ketone–hydroxyapatite–carbon nanotubes (PEEK‐HAP‐CNTs) nanocomposite. The nanocomposites have been fabricated for biomedical applications using a melt processing at 400°C. The results showed that CNTs increase the effective contact area between PEEK and HAP in the nanocomposite. The addition of 0.1 wt% CNTs to the composite led to an elastic modulus and compressive strength improvement for 13% and 31% compared to PEEK‐HAP. The scanning electron microscopy images showed the microstructure of the composites. The results of cell attachment, alkaline phosphatase, spreading, proliferation, and alizarin red tests showed that adding CNT into the composite improved the function of MG‐63 cells. In conclusion, PEEK‐HA‐CNT is more suitable to be used as an implant material than PEEK and PEEK‐HA composites.