One of the promising liquid cooling techniques for microelectronics is attaching a microchannel heat sink to, or directly fabricating microchannels on, the inactive side of the chip. A stacked microchannel heat sink integrates many layers of microchannels and manifold layers into one stack. Compared with single-layered microchannels, stacked microchannels provide larger flow passages, so that for a fixed heat load the required pressure drop is significantly reduced. Better temperature uniformity can be achieved by arranging counterflow in adjacent microchannel layers. The dedicated manifolds help to distribute coolant uniformly to microchannels. In the present work, a stacked microchannel heat sink is fabricated using silicon micromachining techniques. Thermal performance of the stacked microchannel heat sink is characterized through experimental measurements and numerical simulations. Effects of coolant flow direction, flow rate allocation among layers, and nonuniform heating are studied. Wall temperature profiles are measured using an array of nine platinum thin-film resistive temperature detectors deposited simultaneously with thin-film platinum heaters on the backside of the stacked structure. Excellent overall cooling performance (0.09°C∕Wcm2) for the stacked microchannel heat sink has been shown in the experiments. It has also been identified that over the tested flow rate range, counterflow arrangement provides better temperature uniformity, while parallel flow has the best performance in reducing the peak temperature. Conjugate heat transfer effects for stacked microchannels for different flow conditions are investigated through numerical simulations. Based on the results, some general design guidelines for stacked microchannel heat sinks are provided.