Understanding the biodegradability of graphene materials by the action of oxidative enzymes secreted by immune cells is essential for developing applicable biomedical products based on these materials. Herein, we demonstrate the biodegradation of graphene oxide (GO) by recombinant eosinophil peroxidase (EPO) enzyme extracted from human eosinophils in the presence of a low concentration of hydrogen peroxide and NaBr. We compared the degradation capability of the enzyme on three different GO samples containing different degrees of oxygen functional groups on their graphenic lattices. EPO succeeded in degrading the three tested GO samples within 90 h treatment. Raman spectroscopy and transmission electron microscopy analyses provided clear-cut evidence for the biodegradation of GO by EPO catalysis. Our results provide more insight into a better understanding of the biodegradation of graphene materials, helping the design of future biomedical products based on these carbon nanomaterials.