Background No existing longitudinal data document exercise performance after pediatric heart transplantation. We report the exercise performance findings from the longitudinal study of pediatric heart transplantation patients and the association of aerobic capacity with echocardiographic measures of graft function. Methods We performed a retrospective analysis of 28 children after heart transplantation who underwent 87 exercise tests and echocardiograms. Subjects exercised using graded cycle or treadmill protocols. Maximal oxygen consumption (VO 2), physical working capacity, peak heart rate, and anaerobic threshold were evaluated. To measure systolic and diastolic function, shortening fraction and mitral valve pressure half-time (PHT) respectively, were obtained by echocardiography. Results The average age at transplantation was 10.9 ± 5.6 years, at initial exercise test was 13.8 ± 5.0 years, and at final exercise test was 15.8 ± 5.2 years. Percent-predicted values at the initial exercise test were VO 2, 59.3%; physical working capacity, 60.2%; and peak heart rate, 75.8%; these remained similarly decreased at the final exercise test. Shortening fraction and PHT were within normal limits, but PHT was significantly greater at final test ( p < 0.05). The relationship of VO 2% with time was statistically significant, described by a quadratic equation that included initial VO 2% and time from heart transplantation. This relationship remained significant when the shortening fraction ( p < .05) but not PHT was added as a covariate in the equation. Conclusions Exercise performance after pediatric heart transplantation is impaired and, despite an initial improvement, declines over time. This can be explained by increasing diastolic dysfunction independent of donor graft age. If confirmed, these findings point the direction to further research aimed at limiting this aerobic capacity decline after heart transplantation.