Open-cell nanoporous Au (np-Au) electrodes with pore size of approximately 40 nm were fabricated by dealloying of Au–Ag, and surfaces of the electrodes were modified with a self-assembled monolayer (SAM) of 4-aminothiophenol to enhance the electrocatalytic activities of immobilized laccase and glucose oxidase. Enzyme-immobilized SAM-modified np-Au working electrodes exhibited additional reduction–oxidation peak pairs in cyclic voltammograms in buffer solution (pH = 5.0). Thus, the SAM on the np-Au facilitated electron transfer between the electrode and reactants. First-principles calculations of perfect and defective Au (111) surfaces indicated that the atomic defects at nanoligament surface of np-Au are critically responsible for the electron transfer enhancement. For the utilization of these results, a glucose/O2 biofuel cell composed of these enzyme-immobilized SAM-modified np-Au electrodes was preliminarily fabricated, and it exhibited a maximum power density of 52 μW/cm2 at 20°C. Further optimization of nanoporous structures and kinds of SAM will improve the performance of biofuel cells.