Patients who have undergone the Fontan procedure are at risk for thrombosis, ventricular dysfunction, and valve regurgitation, but data to guide the medical treatment and prevention of these adverse outcomes in this population are lacking. This analysis examined medication usage among Fontan patients by putative indication and by study center. The medical history and current medications of 546 Fontan subjects, ages 6-18 years, were assessed in a Pediatric Heart Network multicenter cross-sectional study. Cardiac imaging was performed within 3 months of enrollment. The majority of the subjects (64%) were taking two or more medications. Antithrombotics were taken by 86% of those with a history of stroke, thrombosis, or both and 67% of those without such a history (P = 0.01). Conversely, 14% of those with a history of stroke, thrombosis, or both were taking no antithrombotic. Angiotensin-converting enzyme inhibitor (ACEi) therapy was independently associated with moderate or severe atrioventricular valve regurgitation (P = 0.004), right ventricular morphology (P < 0.001), and shorter time since Fontan (P = 0.004) but not with ventricular systolic dysfunction. Glycoside therapy and diuretic therapy each was associated with older age at Fontan (P = 0.001 and P = 0.023, respectively) and a history of post-Fontan arrhythmia (P < 0.001 and P = 0.003, respectively) but not with ventricular systolic dysfunction. Medication use rates varied widely among the centers, even with controls for center differences in patient characteristics. Prospective therapeutic trials are needed to guide the medical treatment of Fontan patients.