Background: Many congenital heart diseases (CHD) are associated with genetic defects. Children with complex CHD often have heart failure requiring heart transplant. Given the broad spectrum of genetic pathologies and dearth of transplants performed in these children, little is known regarding their outcomes. Methods: We conducted a retrospective review of heart transplants performed at a high-volume center from 2007 to 2021. Patients were separated into pathogenic molecular and copy number variants, aneuploidies, and variants of uncertain significance, and compared with patients without known genetic diagnoses. Variables included genetic diagnoses, bridge-to-transplant approach, preoperative comorbidities, operative characteristics, and postoperative complications. Outcomes included intensive care unit-free days to 28 days, hospital mortality, survival, rejection, retransplantation, and educational status at latest follow-up. Results: In all, 223 patients received transplants over the study period: 9.9% (22 of 223) had pathogenic molecular variants; 4.5% (10 of 223) had copy number variants; 1.8% (4 of 223) had aneuploidies; and 9% (20 of 223) had variants of uncertain significance. The most common anomalies were Turner syndrome (n = 3) and 22q11.2 deletion syndrome (n = 2). Children with aneuploidies had higher rates of hepatic dysfunction and hypothyroidism, whereas children with pathogenic copy number variants had higher rates of preoperative gastrostomy and stroke. Children with aneuploidies were intubated longer after transplant, with greater need for reintubation, and had the fewest intensive care unit-free days. Mortality and mean survival did not differ. At median follow-up of 4.4 years (range, 1.9 to 8.8), 89.7% of survivors (26 of 29) with pathogenic anomalies were attending or had graduated school. Conclusions: Despite more preoperative comorbidities, midterm outcomes after heart transplant in children with genetic syndromes and disorders are promising.