Here, we demonstrate a modular, reconfigurable, and self-sufficient convective heat exchanger for regulation of temperature in microfluidic systems. The heat exchanger consists of polymer tubes wrapped around a plastic pole and fully embedded in an elastomer block, which can be easily mounted onto the microfluidic structure. It is compatible with various microfluidic geometries and materials. Miniaturized, battery-powered piezoelectric pumps are utilized to drive the heat carrying liquid through the heat exchanger at desired flow rates and temperatures. Customized temperature profiles can be generated by changing the configuration of the heat exchanger with respect to the microfluidic structure. Tailored dynamic temperature profiles can be generated by changing the temperature of the heat carrying liquid in successive cycles. This feature is used to study the calcium signaling of endothelial cells under successive temperature cycles of 24 to 37 °C. The versatility, simplicity, and self-sufficiency of the heat exchanger makes it suitable for various microfluidic based cellular assays.