The monolithic three-dimensional (3D) graphene network is used as the support for Pt nanoparticles (NPs) to fabricate an advanced 3D graphene-based electrocatalyst. Distinct from previous strategies, the monodispersed Pt NPs with ultrafine particle size (∼3 nm) are synthesized using ferritin protein nanocages as the template and subsequently self-assembled on the 3D graphene by leveraging on the hydrophobic interaction between the ferritin and the graphene. Following the self-assembly, the ferritins are removed, resulting in a stable Pt NP/3D graphene composite. The composite exhibits much enhanced electrocatalytic activity for methanol oxidation as compared with both Pt NP/chemically reduced graphene oxide (Pt/r-GO) and state-of-the-art Pt/C catalyst. The observed electrocatalytic activity also shows marked improvement over Pt/3D graphene prepared by pulse electrodeposition of Pt. This study demonstrates that protein nanocage templating and assembly are promising strategies for the fabrication of functional composites in catalysis and fuel cell applications.