The Fontan procedure is the final stage in the palliative surgical approach to patients with single-ventricle physiology. These patients have an increased risk for thromboembolic disease in the Fontan circuit, which can be evaluated by chest computed tomography angiography (CTA) in acute settings. However, false-positive results are common secondary to unusual streaming patterns in the Fontan circuit. A biphasic CTA protocol was evaluated for the capability to clearly identify structures of the Fontan circuit that are critical for the evaluation of thromboembolic disease. The study was a retrospective chart review of Fontan patients with a chest CTA scan obtained between 2011 and 2017. Two pediatric cardiologists with additional training in cardiac CT imaging independently reviewed each CTA and awarded one point for each of 5 Fontan circuit structures clearly identified resulting in a score range of 0–5. A score of 0–2 considered not capable, 3–4 partially capable, and 5 capable to clearly identify critical structures of the Fontan circuit. During the study period, 46 CTA scans were performed on 21 patients. Of the CTA scans using a biphasic protocol, 62.5% (10/16) were considered capable to clearly identify all 5 critical structures of the Fontan circuit vs 27% (8/30) of the CTA scans using a monophasic protocol (p = 0.027). Overall our results suggest that the single-site biphasic CTA protocol has greater diagnostic capability to detect the presence of Fontan thromboembolic disease when compared to the more traditional monophasic CTA protocol. Future prospective studies are needed to confirm these findings.