This study investigates the thermal performance of square pin-fin heat sinks for different operating conditions including different heat flux and different Reynolds numbers. Two heat sinks with different sizes of copper square pin-fins cross section (2-mm fins and 500-μm fins) in-line arranged are experimentally investigated to determine their thermal performance quantified in terms of thermal resistance. The investigation is carried out for a Reynolds numbers between 80 and 470, and heating rate between 21.9–46.7 W. The results indicate that the thermal resistance is lower for micrometer sized fins for smaller Reynolds number as compared to millimeter sized. However, for the larger Reynold numbers, thermal resistance of millimeter sized fins was observed to be lower. The fluid velocity plays a very important role in heat transfer, and it has more pronounced effect on the thermal resistance compared to the fins size.