3D transesophageal echocardiography (3D-TEE) has proven useful and accurate during some operating room (OR), interventional cardiac catheterization (Cath), and electrophysiologic (EP) procedures. The use of 3D-TEE during similar procedures in patients who have undergone Fontan surgery and its additional value have not been previously reported. To determine if live 3D-TEE during procedures post Fontan has added value, 3D-TEEs in 58 post-Fontan patients over a 5-year study period were reviewed. Additional information provided by 3D-TEE (over 2D-TEE) was classified into the following: A: new information which changed/refined the plan and 0: no new important information. Pre- and post-bypass OR 3D-TEEs were counted as one study. A total of 67 3D-TEEs (41 Cath, 13 OR, and 13 EP procedures) were performed. Median age was 14 years (6–39 years). Median weight was 47 kg (21–109 kg). In Cath procedures, only 2/41 (5%) were graded A (R to L atrial level shunt [Fontan leak], n = 1; thrombus in pulmonary artery stump, n = 1). In the OR, 6/13 (46%) were graded A (atrioventricular valvuloplasty, n = 1; neo-aortic valvuloplasty, n = 1; relief of systemic and pulmonary venous outflow obstruction, n = 2 and n = 2; respectively). In EP procedures, 4/13 (31%) were graded A (thrombus, n = 3; mapping for lead placement to assist in multisite pacing for dyssynchrony, n = 1). 3D-TEE of Fontan improved visualization and frequently added value in the OR/EP lab and may be helpful in select catheterization cases. Future studies with a larger sample could build on this data to identify when 3D-TEE will be most useful.