The effect of variable cross-sectional flow area owing to the change in protrusion height along the flow direction, on the thermo-hydraulic performance was studied experimentally. A steady-state study that utilised single-phase water as the working fluid was conducted for Reynolds number range between 1100 and 4400, with a constant heat input of 1000 W along the microchannel length of 30 mm. Two microchannel configurations, namely (a) contracted cross-sectional flow area and (b) expanded cross-sectional flow area, were investigated together with a plain microchannel to evaluate the thermo-hydraulic performance. The average hydraulic diameters of the annular microchannels are kept constant at 600 µm for both configurations. The microchannel with an expanded cross-sectional flow area yielded the highest Nusselt number of 49.6 at Reynolds number of 4377. The same microchannel achieved the highest thermo-hydraulic performance index of 1.59 at Reynolds number of 1974, using the plain microchannel as the reference.