This paper presents a techno-economic analysis of fuel-cell-based auxiliary power units (APUs), with emphasis on applications in the trucking industry and the military. The APU system is intended to reduce the need for discretionary idling of diesel engines or gas turbines. The analysis considers the options for on-board fuel processing of diesel and compares the two leading fuel cell contenders for automotive APU applications: proton exchange membrane fuel cell and solid oxide fuel cell. As options for on-board diesel reforming, partial oxidation and auto-thermal reforming are considered. Finally, using estimated and projected efficiency data, fuel consumption patterns, capital investment, and operating costs of fuel-cell APUs, an economic evaluation of diesel-based APUs is presented, with emphasis on break-even periods as a function of fuel cost, investment cost, idling time, and idling efficiency. The analysis shows that within the range of parameters studied, there are many conditions where deployment of an SOFC-based APU is economically viable. Our analysis indicates that at an APU system cost of $ 100kW−1, the economic break-even period is within 1 year for almost the entire range of conditions. At $ 500kW−1 investment cost, a 2-year break-even period is possible except for the lowest end of the fuel consumption range considered. However, if the APU investment cost is $ 3000kW−1, break-even would only be possible at the highest fuel consumption scenarios. For Abram tanks, even at typical land delivered fuel costs, a 2-year break-even period is possible for APU investment costs as high as $ 1100kW−1.