In this work the optimization-based, integrated concurrent design method is applied to the modelling, analysis, and design of a transportation fuel cell system. A general optimal design model considering both functional performance and production costs is first introduced. Using the Ballard Mark V Transit Bus fuel cell system as an example, the study explores the intrinsic relations among various fuel cell system performance and cost aspects to provide insights for new cost-effective designs. A joint performance and cost optimization is carried out to demonstrate this new approach. This approach breaks the traditional barrier between design (concerning functional performance) and manufacturing (conceming production costs), allowing both functional performance and production costs to be fed into design phase and to be jointly optimized.