This paper investigates how a constant magnetic field between the anode catalyst and the electrode surface affects the performance of an enzymatic biofuel cell. Molecular dynamics techniques were employed to observe the nanoscale proton transport phenomenon. The simulation model comprised a Au electrode, pyrroloquinoline quinine, flavin adenine dinucleotide, and glucose macromolecules with hydronium ions in aqueous solution. A constant magnetic field was applied parallel to the anode electrode surface in the simulation process. It is found that the magnetic field is able to enhance the hydronium mobility in the solution and the rate of the biochemical reaction increased. Simulation results show that the hydronium diffusivity increases from to a maximum at a glucose concentration of 27 mM and from to a maximum at a glucose concentration of 82 mM.