Heparin is used to decrease the risk of thromboembolic complications during electrophysiology studies (EPS); however, there is wide practice variation and minimal evidence to guide heparin dosing, particularly in pediatric patients. This study retrospectively analyzed heparin dosing and response, measured via activated clotting time (ACT), in patients undergoing EPS and used these data (pre-protocol cohort, n = 40), as well as guidance from available literature to implement a standardized heparin protocol (phase 1, n = 43). We utilized quality improvement methodology to refine this protocol (phase 2, n = 40) to improve therapeutic heparin response. Prior to the protocol, patients achieved therapeutic ACT levels (250-350 s) only 35% of the time which improved to 60% during phase 1 (p < 0.05) and to 73% during phase 2 (p < 0.001 compared to pre-protocol). There were no thromboses or significant adverse events in any group. These results demonstrate the effectiveness of a standardized heparin protocol in achieving effective antithrombotic therapy during left-sided pediatric EPS.