The electronic control unit (ECU) in electrical powered hybrid and fuel cell vehicles is exceedingly complex. Rapid prototyping control is used to reduce development time and eliminate errors during software development. This paper describes a high-efficiency development method and a flexible tool chain suitable for various applications in automotive engineering. The control algorithm can be deployed directly from a Matlab/Simulink/Stateflow environment into the ECU hardware together with an OSEK real-time operating system (RTOS). The system has been successfully used to develop a 20-kW fuel cell system ECU based on a Motorola PowerPC 555 (MPC555) microcontroller. The total software development time is greatly reduced and the code quality and reliability are greatly enhanced.