This study focuses on the optimal configuration and suitable flow rate in photovoltaic thermal (PV/T) system. Design and verification were carried out by finite element method (FEM) to solve computational fluid dynamic (CFD) problem and to determine the suitable flow in a collector system. COMSOL MULTIPHYSICS® software was used for the analysis. The computed results were then comparatively evaluated against a set of result samples obtained from testing data of the 16 modules of PV/T system—a configuration with 4 strings (horizontal-axis) of 4 modules in-series (vertical-axis) (4×4). The redesign of PV/T system was further studied by changing the system configuration from a 4×4 configuration to simulate various configurations consisting of 8×2, 3×4, 4×3 and 6×2. For the same number of PV/T module (16), the 4×4 configuration provided better flow distribution, when compared with an 8×2 configuration. When decreasing to 12 modules, it was shown that the 3×4 configuration resulted in the most suitable flow distribution, compared with the 4×3 and 6×2 configurations. From these results, it can be concluded that the number of strings used was inversely proportional to the flow distribution quality. Experimental results have also shown that the optimized flow rate for the 4×4 configuration was approximately 1–3 L/min.