Cardiopulmonary bypass (CPB) is routinely used for performing congenital heart operations. While most congenital heart operations can be performed with bypass times under 2 hours, complex pulmonary artery reconstructions require longer periods of CPB to facilitate the surgical repair. This article is intended to summarize the surgical and perfusion techniques utilized in patients undergoing complex pulmonary artery reconstructions at our institution. The initial portion of this manuscript provides an in-depth description of the surgical techniques employed for pulmonary artery reconstructions. This information is important in order to understand why prolonged CPB is a necessary requirement. The manuscript then provides a detailed description of the perfusion techniques and the modifications to the CPB circuit. Finally, the manuscript provides a summary of data from a clinical study evaluating the application of these techniques in 100 consecutive children undergoing complex pulmonary artery reconstruction. The data from this study demonstrated that there was a poor correlation between duration of CPB and both the number of postoperative complications and hospital length of stay. Major adverse cardiac events occurred in 11 (11%) patients with one hospital mortality. These results suggest that prolonged CPB does not predispose to adverse outcomes in this select population of patients.