Numerical study has been carried out to examine the heat transfer and fluid flow characteristics of open microchannel heat sinks consist of square pin fins. Variation of fin height evolves an open configuration of microchannel having open space available between fin top surface and top wall of the heat sink. Comparative analysis has been done amongst seven different heat sinks of varying fin height in the range of 0.5–2.0 mm with an increment of 0.25 mm. Fin height of 2.0 mm constitutes completely closed microchannel heat sink i.e. conventional configuration which has been considered to compare the performance with open heat sinks. Single phase liquid water flows through the microchannel where Reynolds number ( Re ) varies from 100 to 800. Uniform heat flux in the range of 75–150 kW/m 2 is supplied to heat the microchannel. Comparative results of overall thermal performance have been presented to recognize the best configuration of the heat sink in the present ranges of operating conditions. Predicted results confirm that increasing the fin height in heat sink; augments the heat transfer rate however, it persists only up to 1.5 mm of fin height. Beyond this height of the fin, i.e. for 1.75 mm and 2.0 mm, heat dissipation capacity of the heat sink drops. Moreover, heat sinks of shorter fins (0.5–1.00 mm) depict considerably low thermal performance nevertheless; pressure drop is also lower in such configuration and increases with fin height. Superiority of the heat sink having fin height of 1.5 mm is also revealed through thermal performance factor and it is attributed to net convective surface area and availability of the open space that facilitates favourable flow behaviour for better heat transfer.