Objectives: To assess variation in outcome measures and their associations with shunt thrombosis prophylaxis regimens after systemic-to-pulmonary artery shunt surgery across centers in the United States participating in the Pediatric Health Information System database. Methods: We reviewed data on neonates who underwent an off-pump shunt procedure at 39 centers between 2000 and 2011. The overall variation in rates of discharge mortality and shunt-related complications were assessed by funnel plots. Complications were defined as revision/repeat of the shunt procedure during the same admission, institution of extracorporeal membrane oxygenation after surgery, and catheter interventions after shunt surgery. Bayesian hierarchical modeling was used to identify outliers. Shunt thrombosis prophylaxis regimens including the time of initiation of aspirin were compared between high and low outliers. Results: A total of 2058 index operations were identified. Funnel plots highlighting the outcomes from various centers allowed discrimination of discharge mortality and complication rates around an aggregate of 6.7% and 12.3%, respectively. Bayesian modeling showed the presence of substantial variation in complication rates between centers; 20% of them were identified as outliers. Aspirin was initiated significantly earlier during the hospital course in centers with a lower composite rate of complications than those with higher rates (median initiation day of 2 [interquartile range (IQR), 1-3] in low outliers vs 4 [IQR, 3-6] in high outliers; P <.001). Conclusions: A substantial variation was found between hospitals in the rate of shunt-related complications. Centers with best outcomes implement aspirin earlier in their postoperative shunt thrombosis prophylaxis regimen.