Three-dimensional numerical simulations were carried out for flow and thermal fields in a minimal unit model of an undulating rectangular duct, which represents the flow passage of a primary surface type heat exchanger core. The effects of the duct undulation amplitude and the duct aspect ratio on the flow and thermal fields are the major interests in this study. The governing equations are the time-dependent, three-dimensional incompressible Navier-Stokes, energy and continuity equations and are discretized using the finite difference method. SIMPLEC algorithm is used for the computation of pressure correction in the iterative procedure. Boundary fitted coordinates (BFC) and a collocated grid system are employed. The computational conditions were set based on the results of System analysis of an SOFC/MGT hybrid system. Calculations were conducted in the Reynolds number range of 100<Re<400 varying the duct aspect ratio, W/H=1.0, 2.0 and the duct undulation amplitude, A/H=0-1.0 while keeping all the other geometric parameters constant. It is found that the overall Nusselt number of the undulated duct is higher than that of a plain straight duct, if the duct cross-sectional aspect ratio is kept constant. The value of the overall Nusselt number is found to be higher for a larger duct undulation amplitude case. Overall Nusselt number shows Reynolds number dependency and its value increases as Re is increased. When the overall performance is evaluated in terms of the pumping power and overall Nusselt number, the larger duct undulation amplitude case shows the better heat transfer performance.