In this article, we report the use of nanochannel arrays as supports for proton exchange membranes in microfluidic fuel cells. The proposed design has been demonstrated by fabricating a sodium silicate based sol–gel structure within such an array bridging two microchannels containing the fuel (HCOOH) and the oxidant (KMnO4) streams. A voltage was generated in this system by bringing two platinum electrodes in contact with these solutions and then connecting them through an external circuitry. With this current design, we have been able to generate an open circuit potential of 1.31V and a maximum current of 31.2μA at 25°C.