Microchannel heat dissipation devices were first conceptualized in 1981 and since then are at the forefront of cooling techniques for a variety of applications, extending from computer chips and turbine blades to lasers and optical systems. However, much of the research is concentrated on steady flow of a cooling fluid through the channels. In this article, transient two-dimensional (2D) simulation for heat transfer in microchannels under a pulsed-flow condition is carried out. For validation of simulation results, a novel heat sink device is designed and fabricated, using milling and micro-electric discharge machining (EDM) technique. The fabricated device is then tested to evaluate the effect of a variable flow rate on the heat transfer characteristics when the flow is pulsating. It is found that the numerical results underpredict slightly as compared to actual experimental results. Results indicate a higher temperature at the outlet of the heat sink device for lower pulse frequency, and as pulse frequency increases, the outlet temperature decreases. © 2021 SAGE Publications.