Utilization of a heat source to regulate the shock wave–boundary layer interaction (SWBLI) of hypersonic inlets during throttling was computationally investigated. A plug was installed at the intake isolator’s exit, which caused throttling. The location of the heat source was established by analysing the interaction of the shockwave from the compression ramp and the contact spot of the shockwave with that of the inlet cowl. Shockwave interaction inside the isolator was investigated using steady and transient cases. The present computational work was validated using previous experimental work. The flow distortion (FD) and total pressure recovery (TPR) of the inflows were also studied. We found that varying the size and power of the heat source influenced the shockwaves that originated around it and affected the SWBLI within the isolator. This influenced most of the performance measures. As a result, the TPR increased and the FD decreased when the heat source was applied. Thus, the use of a heat source for flow control was found to influence the performance of hypersonic intakes.