A novel fabrication technique for micro proton exchange membrane fuel cells (μPEMFCs) based on carbon-MEMS (C-MEMS) was optimized to yield higher performance cells. Polymer manufacturing is relatively easy compared to directly patterning graphite as is typically done to make fuel cell bipolar plates. In a C-MEMS approach, fuel cell bipolar plates are fabricated by first patterning polymer Cirlex® sheets. By subsequently pyrolyzing the machined polymer sheets at high temperature in an inert atmosphere, carbon bipolar plates with intricate groove structures to distribute the reactants are obtained. Using an improved assembly technique such as polishing the carbonized plates to minimize the contact resistance between gas diffusion layers (GDL) and bipolar plates, better pyrolysis temperature control and a better end plate design, a μPEMFC with a 0.64cm2 active surface was fabricated using the newly developed bipolar plates. At 1atm and 25°C a maximum power density of ∼76mWcm−2 was obtained, and at 2atm and 25°C ∼85mWcm−2 was achieved. These data are comparable with data reported in the literature for μPEMFCs and are a dramatic improvement over earlier results reported for the same C-MEMS based fuel cell. Electrochemical Impedance Spectroscopy (EIS) and cyclic voltammetry were carried out to characterize steady-state and transient characteristics of the novel C-MEMS fuel cell.