There has been a recent uptake in the use of polyether-ether-ketone (PEEK), which is an organic thermoplastic polymer, in the manufacturing of various medical devices, implants, and equipment. Finding the best time and procedure for PEEK after sulfonation is the goal of this research. A total of 30 PEEK discs were sulfonated in this study by immersing them in concentrated (H2SO4) sulfuric acid for various durations and subsequently treated using various post-treatment techniques. Five experiments were carried out, aimed studying the effect of immersion time (5 s–2 min). The methods used as post-treatment were hydrothermal treatment, immersion in NaOH, and washing with acetone. The sulfonation time was measured, and the post-treatment techniques, surface characterizations, were conducted using scanning electron microscopy (SEM) (Electron Optics Instruments, LLC., West Orange, NJ, USA), atomic force microscopy (AFM) (AFM, Vía Burton, CA, USA), and hydrophilic properties. The results were confirmed by attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). The findings of this study demonstrate that sulfonating PEEK caused a structure with a porous network to form in every sample. As the sulfonation time increased, the porous structure became more noticeable and the concentration increased. As a consequence, the roughness of the surface increased notably, and the modified PEEK surface’s wettability improved noticeably. Hydrothermal treatment was determined to be the most successful way for eliminating the leftover sulfuric acid, and sulfonation for 2 min was determined to be ideal. By understanding the best post-treatment procedures and ideal sulfonation duration, a theoretical foundation for the production of sulfonated PEEK for orthopedic uses may be laid.