In this work the optimization-based, integrated concurrent design method is extended to a general mechanical system — the transportation fuel cell system. A general optimal design model considering both functional performance and production costs is first introduced. Mathematical models of the functional performance and production costs of the Ballard fuel cell system are then discussed. A joint performance and cost optimization is carried out using the Ballard fuel cell system to demonstrate the approach. The optimization concurrently takes into account of two functional performance aspects and production costs to identify the optimal values of two key design variables. The work is a continuation of the authors’ earlier research on integrated concurrent engineering design.