Background Heart transplantation remains a resource-intensive therapy for children. However, data regarding change in costs over time are scarce. We tested the hypothesis that hospital charges for pediatric heart transplant hospitalizations would increase from 1997 to 2006 and assessed factors associated with hospital charges. Methods A retrospective analysis of the Healthcare Cost and Utilization Project Kids' Inpatient Database was performed on admissions surrounding heart transplantation for the years 1997, 2000, 2003, and 2006. The database is a nationwide sampling of pediatric hospital discharges and is weighted to provide national estimates. Results There were 353 (95% confidence interval, 201–505) pediatric heart transplants in 1997 and 355 (95% confidence interval, 226–485) in 2006. Mean hospital charges increased from $279,399 in 1997 to $451,738 in 2006 (p < 0.001). This increase was similar to that observed for other pediatric surgical diseases. Increases also occurred in morbidities, including pulmonary hypertension (p = 0.04) and sepsis (p = 0.04), and in the use of extracorporeal membrane oxygenation (p = 0.03). On multivariable analysis, greater hospital charges were associated with later calendar year (p = 0.001), stroke (p = 0.03), sepsis (p = 0.001), renal failure (p = 0.008), arrhythmia (p = 0.03), and use of extracorporeal membrane oxygenation (p < 0.001) and ventricular assist device (p < 0.001). Conclusions From 1997 to 2006, mean charges for pediatric heart transplant hospitalizations increased by > $170,000 (160%). Although greater morbidities in the later years of the study potentially contributed to increased charges, later calendar year was independently associated with increased charges. The changes in charges for heart transplant are similar to the increases seen in other surgical procedures. Ongoing study of management strategies is needed to determine cost-effective therapies for this complex group of patients.