To investigate the reactive species generated in the pyrite (FeS2)-activated persulfate (PS) process, typical antiepileptic carbamazepine (CBZ) was chosen as the target contaminant and then degraded in the FeS2/PS system. Optimum operating conditions were determined to be 0.5 g·L−1 of FeS2 dosage and 1 mM of PS concentration via response surface method analysis. Different from previous conclusions that Fe(II) reacted with PS to directly generate sulfate radical (SO4−), tetravalent iron [Fe(IV)] was identified as a reactive intermediate employing PMSO probe, and the highest steady state concentration of Fe(IV) was calculated to be 5.62 × 10−4 μM at pH 7.0. Conversely, the highest steady state concentrations of SO4− and hydroxyl radical (OH) occurred at pH 3.5 as well as the complete removal of CBZ (21.16 μM). Alcohol quenching experiment and competitive oxidation experiment confirmed that SO4−, OH and Fe(IV) all contributed to CBZ degradation. According to X-Ray photoelectron spectroscopy spectra and density functional theory calculations, it demonstrated the electron transfer between the S atoms and the Fe site which absorbed PS molecule, thus contributing to the formation of heterogeneous Fe(IV). In the proposed CBZ degradation pathways, Fe(IV) gave rise to the primary product 10,11-epoxycarbamazepine formation, and radical species continued to degrade and mineralize 10,11-epoxycarbamazepine.