This paper presents the study of infrared (IR) reflow oven characteristics for suitable operating conditions of the flexible printed circuit board (FPCB) in the reflow soldering process. A computer-based model that imitates a real-time oven was developed with practical boundary conditions. Since the radiation effect is dominant in the reflow process, a discrete ordinate (DO) model was selected to simulate the effect. The experimental work acts as a benchmark and the reflow profile was set to follow the standards of JSTD-020E. The simulation of the model has a great consensus between the experimental data. It was found that the temperature distribution was inhomogeneous along with the phases. The FPCB surface also has a higher surface temperature than oven air during the operating reflow profile. An in-depth study using the simulation approach reveals that the temperature distribution of the desktop reflow oven is dependent on several factors, namely fan speed, FPCB position, and FPCB thickness. The rotational fan generates an unsteady flow that induces inhomogeneous temperature at different positions in the reflow oven cavity. The results are useful for studying further improvements to achieve temperature uniformity within the oven chamber.