Here we report fabrication of tiny on-chip fuel cells on polymer films. Since on-chip cells which we have so far fabricated on silicon substrates through a series of microfabrication procedures are of a simple microchannel-based design, their fabrication on a polymer substrate by molding is attractive in terms of the rapid fabrication and of the inexpensive fabrication procedures and materials. To do so, a nickel mold was first prepared by electroplating from the conventional silicon-based cell, i.e., a master, and then the cell was replicated on cycloolefin polymer films by hot embossing. The microchannel thus replicated on the polymer film was confirmed to be almost identical to the silicon master by observation with a confocal microscope. Finally, Au current collectors sufficiently adhesive to the polymer were successfully deposited after the surface modification by an oxygen plasma treatment.