Several device designs for cavopulmonary mechanical circulatory support (MCS) are under investigation, however, challenged by the Fontan population’s heterogeneity in size, cardiovascular and thoracic anatomy. This study aimed to preclinically assess the anatomical compliance of proposed device designs in silico. Representative double- and single-outlet cavopulmonary assist device (CPAD) designs were virtually implanted into CT imaging data of 10 patients previously palliated with total cavopulmonary connection (TCPC) for functionally univentricular hearts. Anatomical device compatibility was characterized concerning pump proximity to cardiovascular, respiratory and thoracic structures, as well as pump in- and outflow graft configuration. In 10 Fontan patients with a median age of 10.4 years (interquartile range [IQR] 5.0–15.3 years) and a median body surface area of 1.09 m2 (IQR 0.76–1.28 m2), implantation of a double-outlet CPAD was feasible in 1 patient (10%). In all other, adverse device intersection with the trachea and (neo-)aorta, or posterior pulmonary artery outflow graft kinking were observed. A single-outlet design permitted enhanced device mobilization adapting to individual anatomical conditions, resulting in device fit in nine of 10 patients (90%). Despite vast anatomical variations among single ventricle patients, a single-outlet device design may provide intracorporeal cavopulmonary MCS to a broad spectrum of failing Fontan patients.