In the present work, we have reported the synthesis of 3D graphene structures by simple chemical reduction method for application in microbial fuel cell (MFC) as an anode. The synthesis procedure includes synthesis of graphene oxide by modified Hummers method followed by simultaneous reduction of graphene oxide and the formation of hydrogels. The 3D graphene structures are characterized using X-ray diffraction and Raman spectroscopy techniques. Electrochemical characterization is carried out to study the capacitive properties and impedance studies of electrodes in conductive electrolyte. 3D graphene electrodes show remarkably high capacitive current, charge storage and lower charge transfer resistance as estimated through cyclic voltammetry and Nyquist plots. In order to evaluate the performance of 3D graphene electrodes in MFC, power density and polarization curves are recorded in three configurations by varying terminal electron acceptors (TEA) viz., dissolved oxygen (MFC-DO), potassium ferricyanide and MFC without TEA (MFC-NDO). 3D graphene electrodes exhibits maximum power density of 0.49 mW/m2 in potassium ferricyanide followed by MFC-DO (0.36 mW/m2) and MFC-NDO (0.34 mW/m2). Present work highlights the viability of chemically synthesized 3D graphene electrodes as an efficient anode material in MFC.