The channel-to-channel heat flux variation was studied by solving numerically the conjugate, three-dimensional, transient heat transfer problem of louvered fins bounded by multiport aluminum plates. Two different multiport plate configurations (A and B) were analyzed while the geometry of fins was kept constant. Configuration A had 11 round channels of 1.2 mm in diameter and Configuration B had 22 square channels of 0.54 × 0.54 mm2 each. Free stream air velocities analyzed were 1–5 m/s (ReLp = 82–410), and incoming air temperature was 20 °C and 30 °C at constant wall temperature of 10 °C. Numerical results show that heat flux flow downstream from the leading edge was dependent on geometrical parameters (size and number of channels, dimensions of fins) and the properties of air flow (incoming flow velocity, temperature and air flow morphology within the louvered fins domain). The overall heat flux difference between the leading channel and the trailing one was 73% at air velocity of 5 m/s, while this difference was almost 96% at 1 m/s for plate B. Multiport plate A had a heat flux difference between the first and the last channel of 68.7% and 93.8% at 5 m/s and 1 m/s respectively. The magnitude of heat flux at ΔT = 10 K (T = 20 °C) was two times smaller compared to the case of ΔT = 20 K (T = 30 °C).