This article presents an experimental study of thermo-hydrodynamic phenomena in a microchannel heat exchanger system. The aim of this investigation is to develop correlations between flow/thermal characteristics in the manifolds and the heat transfer performance of the microchannel. A rectangular microchannel fabricated by a laser-machining technique with channel width and hydraulic diameter of 87 m and 0.17 mm, respectively, and a trapezoidal-shaped manifold are used in this study. The heat sink is subjected to iso-flux heating condition with liquid convective cooling through the channels. The temporal and spatial evolutions of temperature as well as total pressure drop across the system are monitored using appropriate sensors. Data obtained from this study were used to establish relationships between parameters such as longitudinal wall conduction factor, residence and switching time, and thermal spreading resistance with Reynolds number. Result shows that there exist an optimum Reynolds number and conditions for the microchannel heat exchanger system to result in maximum heat transfer performance. The condition in which the inlet manifold temperature surpasses the exit fluid temperature results in lower junction temperature. It further shows that for a high Reynolds number, the longitudinal wall conduction parameter is greater than unity and that the fluid has sufficient dwelling time to absorb heat from the wall of the manifold, leading to high thermal performance.