This paper presents a dynamic model for studying the cold start dynamics and observer design of an auxiliary power unit (APU) for automotive applications. The APU is embedded with a solid oxide fuel cell (SOFC) stack which is a quiet and pollutant-free electric generator; however, it suffers from slow start problem from ambient conditions. The SOFC APU system equips with an after-burner to accelerate the start-up transient in this research. The combustion chamber burns the residual fuel (and air) left from the SOFC to raise the exhaust temperature to preheat the SOFC stack through an energy recovery unit. Since thermal effect is the dominant factor that influences the SOFC transient and steady performance, a nonlinear real-time sliding observer for stack temperature was implemented into the system dynamics to monitor the temperature variation for future controller design. The simulation results show that a 100W APU system in this research takes about 2min (in theory) for start-up without considering the thermal limitation of the cell fracture.