By providing the key carbon and nitrogen elements needed for eutrophication, the potential toxicity of ethylenediaminetetraacetic acid (EDTA) prompts the exploration of effective treatment methods to minimize the amount of EDTA released into the environment. In this study, Fe3O4 magnetic nanoparticles (MNPs) were prepared and used as catalysts to study the mineralization of EDTA in Fenton-like reactions under neutral pH. Fe3O4 MNPs were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), and Brunauer–Emmett–Teller (BET). The effects of pH, ferric ion leaching, and H2O2 concentration on chemical oxygen demand (COD) removal of EDTA were investigated. The morphological characterization of the nanoparticles suggests a quasi-spherical structure with small particle size and a surface area of 49.9 m2/g. The results show that Fe3O4 MNPs had good catalytic activity for the mineralization of EDTA under pH 5.0–9.0. The optimum conditions for the COD removal of 45% at pH 7.0 were: 40 mM H2O2, 10 mM Fe3O4, and 1 g/L EDTANa2·2H2O at 303 K. Fe3O4 MNPs maintained high catalytic activity after five cycles of continuous degradation of EDTA. According to reactive oxidizing species measurements obtained by electron spin resonance (ESR), it was confirmed that HO· free radicals, presented in the H2O2/Fe3O4 MNPs heterogeneous Fenton-like reaction, were the primary active group in the removal of EDTA. These features can be considered beneficial to the application of Fe3O4 MNPs towards industrial wastewater treatment.