One of the most difficult issues to fabricate a fuel cell with a complex design is the manufacturing method. To solve this difficulty, the authors applied an innovative method of fuel cell fabrication, i.e., rapid prototyping technology. The rapid prototyping technology can both fabricate the complex design and shorten the fabrication time. In this paper, the authors used a 3D software (CATIA) on the fuel cell design and utilized the rapid prototyping to accelerate the prototype development of complex stack designs and to verify the practicability of the new fabrication for fuel cells. The honeycomb shape methanol reservoir and cathode structure design of a direct methanol fuel cell (DMFC) and the complex flow distributor design of a monopolar air-breathing proton exchange membrane fuel cell (PEMFC) stack, which were almost impossibly manufactured by traditional manufacturing, were made in this study. The performance of the traditional air-pumping DMFC and that of an air-breathing DMFC were compared in this study. The feasibility of a complex pseudobipolar design DMFC stack was also verified. For the miniature air-breathing PEMFC made by rapid prototyping with ABS material, its performance is close to the state-of-the-art compared to previous published literatures (Hsieh et al. 2006, “Study of Operational Parameters on the Performance of Micro PEMFCs With Different Flow Fields,” Energy Convers. Manage., 47, pp. 1868–1878; Schmitz, A., Wagner, S., Hahn, R., Uzun, H., and Hebling, C., 2004, “Stability of Planar PEMFC in Printed Circuit Board Technology,” J. Power Sources, 127, pp. 197–205; Hottinen, T., Mikkola, M., and Lund, P., 2004, “Evaluation of Planar Free-Breathing Polymer Electrolyte Membrane Fuel Cell Design,” J. Power Sources, 129, pp. 68–72). A new solution to manufacture complex fuel cell design, rapid prototyping, has been first applied to the fabrication of complicated flow channels in ABS materials and directly used in both DMFC and PEMFC in this paper. Its feasibility was verified and its promising performance was also proved.