Gemfibrozil (GEM), an acidic pharmaceutical used to reduce plasma triglycerides and total cholesterol levels, persists in conventional wastewater treatment processes. However, understanding its degradation mechanism and kinetics through advanced oxidation processes (AOPs) remains unexplored. Therefore, this study employed density functional theory (DFT) at the M06-2X/6-311++G(3df,2p) //M06-2X/6-311G(d,p) level to theoretically investigate the oxidation of GEM by hydroxyl and sulfate radicals in aqueous environments. Mechanistic pathways, reaction kinetics, and ecotoxicological assessments were conducted. Two distinct mechanisms involving addition and hydrogen abstraction were delineated. The overall rate constants, accounting for diffusion-limited effects, were determined as 1.84 × 109 M−1 s−1 and 7.73 × 109 M−1 s−1 at 298 K for •OH and SO4•−-initiated reactions, respectively. Analysis revealed that hydrogen abstraction at the carboxyl group predominated, while favorable addition occurred at the carbon atom positioned at the 3rd position of the benzene ring. The calculated half-life of GEM initiated by •OH and SO4•− was approximately 377 and 90 s with their concentration of 10−12 mol/L at 298 K. Ecotoxicity assessment via quantitative structure-activity relationship (QSAR) indicated a certain degree of danger posed by GEM and its degradation by-products to aquatic organisms, albeit exhibiting lower toxicity compared to GEM itself.