PEM fuel cell vehicles have been getting much attraction due to a sort of highly clean and effective transportation. The onboard fuel processor, however, is inevitably required to supply the hydrogen by conversion from some fuels since there are not enough available hydrogen stations nearby. A lot of studies have been focused on analyses of ATR reactor under the assumption of thermo-neutral condition and those of the optimized process for the minimization of energy consumption using thermal efficiency as an objective function, which doesn’t guarantee the maximum hydrogen production. In this study, the analysis of optimization for 100 kW PEMFC onboard fuel processor was conducted targeting various fuels such as gasoline, LPG, diesel using newly defined hydrogen efficiency and keeping simply synthesized heat exchanger network regardless of external utilities leading to compactness and integration. Optimal result of gasoline case shows 9.43% reduction compared to previous study, which shows the newly defined objective function leads to better performance than thermal efficiency in terms of hydrogen production. The sensitivity analysis was also done for hydrogen efficiency, heat recovery of each heat exchanger, and the cost of each fuel. Finally, LPG was estimated as the most economical fuel in Korean market.