Overcooling of electronic devices and systems results in excess energy consumption, which can be reduced by closely linking cooling requirements with actual power dissipation. A thermal model-based flow rate controller for single phase liquid cooled single tier and three-dimensional (3D) stacked chips, using pin-fin enhanced microgap was studied in this paper. Thermal compact models of a planar and 3D stacked two-layer pin-fin enhanced microgap were developed, which ran times faster than using full-field computational fluid dynamics/heat transfer (CFD/HT) method, with reasonable accuracy and spatial details. Compact model was used in conjunction with a flow rate control strategy to provide the needed amount of liquid to cool the heat sources to the desired temperature range. Example case studies show that the estimated energy savings in pump power is about 25% compared with pumping fluid at a constant flow rate.