The unique characteristics of polyether ether ketone (PEEK) including low elastic modulus, high mechanical strength, and biocompatibility have made it an attractive alternative for the metallic biomaterials. However, its bioinert property is always the main concern, which could lead to poor osseointegration and subsequent clinical failure of the implant. Changing the surface structure to porous structure and mixing it with bioactive hydroxyapatite (HA) are the common methods, which could be used to enhance the properties of the PEEK‐based implants. In this study, friction stir processing was utilized for the fabrication of porous HA/PEEK surface nanocomposite. Scanning electron microscopic image of the nanocomposite surface showed nano‐scale roughness of the porous structure. Water contact angle test confirmed the increase in the wettability of the treated specimens. In vitro bioactivity test via simulated body fluid solution, initial cell adhesion, cell proliferation, and cell differentiation assay also confirmed the enhancement in bioactivity of the treated surface in comparison to the bare PEEK. This surface modification method requires no special equipment and would not damage the heat‐sensitive PEEK substrate due to the low temperature used during the fabrication process.