Polyetheretherketone (PEEK) has been becoming a popular implant material in orthopaedic applications. The lack of bioactivity affects PEEK’s long-term lifetime, and appropriate surface modification is an effective way to enhance its bioactivity. Sulfonation of PEEK can endow PEEK with a 3 D porous network surface and improve its bioactivity. This study is aimed at exploring an optimal sulfonation time and a post-treatment method of PEEK sulfonation. PEEK was immersed into concentrated sulfuric acid for different sulfonation times and experienced different post-treatment methods to turn into sulfonated PEEK (SPEEK). The immersion times were 0.5 min (SPEEK0.5), 1 min (SPEEK1), 3 min (SPEEK3), 5 min (SPEEK5) and 7 min (SPEEK7), and the post-treatment methods were acetone rinsing (SPEEK-T1), hydrothermal treatment (SPEEK-T2) and NaOH immersion (SPEEK-T3). Scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), Fourier transform infrared spectroscopy, hydrophilic property, ion release and cell viability evaluations were performed to optimize the sulfonation time, and the SEM, EDS, ion release and cell viability were analysed to optimize the post-treatment method. The results showed a porous network structure was formed on all samples of SPEEK, and the porous structure became more obvious and the S concentration increased with increasing sulfonation time. However, too long of an immersion time (SPEEK7) tended to damage the superficial porous structure and left a higher content of sulfuric acid, which could inhibit the growth of MC3T3E1 cells on its surface. In addition, the surface morphology, residual sulfuric acid and cytocompatibility of SPEEK-T1, SPEEK-T2 and SPEEK-T3 were not distinctly different. In conclusion, a 5-min sulfonation time was considered to be the optimal selection, and acetone rinsing, hydrothermal treatment and NaOH immersion showed the same effect in removing the residual sulfuric acid. The understanding of optimal sulfonation time and post-treatment method can provide a theoretical basis in preparing SPEEK for orthopaedic applications.