In recent years, extensive attention has been paid to advanced oxidation processes (AOPs) with peracetic acid (PAA), a widely used disinfectant, using transition metal ions for the degradation of organic contaminants within water environments. Mn(II) has been widely used as an effective homogeneous transition metal catalyst for oxidant activation, but it has shown poor performances with PAA. Since the stability of manganese species can be enhanced through the addition of ligands, this study systematically investigated a novel AOP for the oxidation of carbamazepine (CBZ) using an Mn(II)/PAA system with several different ligands added. The reactive species were explored through UV-vis spectrometry, scavengers, and probe compounds. The results suggest that Mn(III)–ligand complexes and other high-valent Mn species (Mn(V)) were generated and contributed obviously toward efficient CBZ oxidation, while radicals like CH3CO2• and CH3CO3• were minor contributors. The oxidation efficiency of Mn(II)/PAA/ligands depended highly on ligand species, as ethylene diamine tetraacetic acid (EDTA) and oxalate (SO) could promote the oxidation of CBZ, while pyrophosphate (PPP) showed modest enhancement. The results obtained here might contribute to the removal of residue pharmaceuticals under manganese-rich waters and also shed light on PAA-based AOPs that could help broaden our present knowledge of manganese chemistry for decontamination in water treatment.