As an efficient energy resource utilization, fuel cell based auxiliary power unit (FC-APU) system has received attention to reduce greenhouse gas emission and noise for heavy-duty truck idling. The overall system comprises an on-board fuel processor to convert hydrocarbon fuel into hydrogen-rich stream to supply the fuel cell. For efficient and mobile use, an autothermal reforming (ATR) process has been implemented with Ni-based monolithic catalyst. The ATR produces hydrogen through a combination of exothermic and endothermic reactions, balancing the entire process as thermally neutral process. The reforming performance should be examined in order to ensure the reformate gas to supply the fuel cell at proper composition and temperature. Thus, this study proposes a comprehensive mathematical model of diesel ATR involving heat transport and reaction kinetics. The kinetics of the Ni-based catalyst are defined with the refined set of ATR reactions and specific rate parameters found from model-based parameter estimation. The estimation is based on maximum likelihood method with respect to the micro-reactor experimental data. Along with the kinetics, heat transfer phenomena are reflected in the two-dimensional dynamic model. The simulation results are validated with the 1kW-scale diesel ATR reactor. The developed model is used to evaluate the effects of operating conditions and the optimal reactor design is suggested to enhance the reformer performance.