This article presents a design for manufacturing and assembly (DFMA) methodology for estimating the capital costs of new, emerging energy technologies built at varying rates of mass-production. The methodology consists of four major steps: (1) System Conceptual Design, (2) System Physical Design, (3) Cost Modeling, and (4) Continuous Improvement to Reduce Cost. The article describes the application of this methodology to a specific case study of automotive fuel cell systems (FCSs). Because any alternative automotive technology must compete with the very mature and widespread gasoline internal combustion engine, it is vitally important to identify the performance, design, and manufacturing conditions needed to reduce automotive FCS costs. Thus, a DFMA-style analysis is applied to the cost to manufacture a polymer electrolyte membrane (PEM) FCS for cars, at varying rates of production (between 1,000 and 500,000 vehicles per year). The results of this kind of DFMA-style analysis can be used to elucidate key cost drivers at varying levels of production for new energy technologies.