Recirculation for the unreacted fuel is necessary to improve the overall efficiency of the fuel cell system and to prevent fuel starvation since the fuel cell for a vehicle application is a closed system. In case of the automotive fuel cell, the ejector which does not require any parasitic power is good for the performance improvement and easy operation. It is essential to design the customized ejector due to the lack of the commercial ejector corresponding to the operating conditions of the fuel cell systems. In this study, the design methodology for the ejector customized to an automotive fuel cell is proposed. The model based sensitivity analysis prevents the time-consuming redesign and reduces the cost of developing ejector. As a result, the customized ejector to meet the desired performance within overall operating range has developed for the PEMFC automotive system.