Advanced oxidation processes (AOP) have been widely applied in water treatment. However, traditional Fenton reaction based on Fe2+-H2O2 system requires acidic environment and generates large amount of Fe3+ ions. Herein, we reported that magnetic Fe3O4 core-SiO2 shell nanoparticles (Fe3O4@SiO2 NPs) could be used as Fenton-like catalyst for the decomposition of H2O2, resulting in the decoloration of methylene blue (MB). Fe3O4@SiO2 NPs had much higher activity than bare Fe3O4 cores, suggesting the coating of SiO2 enhanced the catalytic activity. Most importantly, the best performance of Fe3O4@SiO2 NPs was observed at neutral pH values. Higher temperature facilitated the diffusion of MB in solution, thus, promoted the decoloration efficiency. The radical reaction nature was reflected by the electron spin resonance spectrum and the significant inhibition of the decoloration in the presence of radical scavenger tertiary butanol. Fe3O4@SiO2 NPs could be magnetically separated and partially regenerated after the decoloration. The implication for the applications of Fe3O4@SiO2 NPs in water treatment is discussed.