Two-dimensional graphene is a promising candidate material for use in high-performance enzymatic biofuel cells (EBFCs). In this work, graphene/enzyme has been integrated onto three-dimensional (3D) micropillar arrays in order to obtain efficient enzyme immobilisation and enhanced enzyme loading and facilitate direct electron transfer. The fabrication process of this system combines top-down carbon microelectromechanical systems (C-MEMS) to fabricate the 3D micropillar array platform and bottom-up electrophoretic deposition (EPD) to deposit the graphene/enzyme onto the electrode surface. The amperometric response of the graphene-based bioelectrode exhibited excellent electrochemical activity, which indicated the successful co-deposition of graphene with the enzymes. The developed 3D graphene/enzyme network-based EBFC generated a maximum power density of 136.3 μW cm⁻² at 0.59 V, which is almost seven times the maximum power density of the bare 3D carbon micropillar array-based EBFC.