Congenital heart disease is exceedingly prevalent in trisomy 13 and 18. Improved survival following congenital heart surgery has been reported, however, mortality remains significantly elevated. Utilizing inpatient data on trisomy 13 and 18 from the 2003–2016 Pediatric Health Information System database, a survival model was developed and validated using data from the California Perinatal Quality Care Collaborative and the California Office of Statewide Health Planning and Development. The study cohort included 1,761 infants with trisomy 13 and 18. Two models predicting survival to 6 months of age were developed and tested. The initial model performed excellently, with a c‐statistic of 0.87 and a c‐statistic of 0.76 in the validation cohort. After excluding procedures performed on the day of death, the revised model's c‐statistic was 0.76. Certain variables, including cardiac surgery, gastrostomy, parenteral nutrition, and mechanical ventilation, are predictive of survival to 6 months of age. This study presents a model, which potentially can inform decision‐making regarding congenital heart surgery.