The in vivo bioactivity of porous polyetheretherketone (PEEK) with a foamed surface was evaluated using rabbit femoral bone. Cylindrical porous PEEK scaffolds, with pore diameter of 550 μm and porosity of 70%, were first prepared and immersed in 98% sulfuric acid, and then washed and immersed in 3 M potassium carbonate solution used as a foaming reagent. Numerous open pores of various sizes, as well as new functional groups, were visualized on the treated PEEK surface by scanning electron microscopy and X-ray photoelectron spectroscopy, respectively. Micro computed tomography (micro-CT) showed that the volumetric density of treated PEEK was higher than that of bare PEEK at 8 weeks after surgery (p<0.05). Additionally, von Kossa staining indicated ingrowth of mature new bone tissue at 4 weeks relative to the bare PEEK group. Our data indicate that surface-treated PEEK exhibited improved bioactivity in vivo.