Microfabricated fuel cell systems have the potential to outperform batteries for man-portable power generation. Because many electronic devices operate at various loads, with frequent start-ups and shut-downs, transient aspects are highly important and must be considered thoroughly. In this paper, the focus is on the optimal start-up of microfabricated fuel cell systems using numerical open-loop optimal control. For start-up purposes, a small rechargeable battery is used to provide the energy needed to heat up the fuel cell stack and meet the power demand when the fuel cell is unavailable or can only satisfy part of the demand. The objective of the start-up problem is to bring the system to a desired operating point with a minimal total mass of the system (battery and fuels), while meeting the nominal power demand at any time and satisfying the operational restrictions. The model for the fuel cell stack consists of partial differential-algebraic equations with multiple time scales and numerical techniques that exploit a separation of these time scales are used for efficient and reliable integration of the state and sensitivity equations. A case study of a microfabricated power generation system employing a high temperature solid-oxide fuel cell and using ammonia and butane as fuels is presented.