Pediatric cardiac fitness and rehabilitation programs vary widely in structure and content. The Cardiac Fitness Program (CFP) is built on traditional training pillars of aerobic, strength, and flexibility, and adds a fourth, training a positive mindset. This study assesses whether the systematic and comprehensive framework of the CFP results in broad benefits for a range of patients with congenital heart disease (CHD). Data from participants between 01/2017 and 12/2022 were analyzed. Pre- and post-CFP cardiopulmonary exercise test parameters, strength and flexibility metrics, and mindset survey results were compared overall, and by sex, age, diagnosis, and hemodynamic level. Of 62 participants (median age 15.5years, range 8 to 23, 50% female), 3% had simple, 37% complex, 24% single ventricle CHD, and 35% arrhythmia, cardiomyopathy, or transplant. Significant improvements were noted in aerobic fitness (mean 9 ± 15% increase in % predicted peak oxygen consumption, p < 0.001). Strength metrics significantly improved (each p < 0.001), as did flexibility (p < 0.001). Patient-reported positive mindset scores did not improve significantly (mean increase 1.8 ± 5.1, p = 0.10, n = 25), whereas parents reported significant improvements (5.9 ± 10.4, p = 0.02, n = 20). Improvements were not significantly different by sex, age, diagnosis, or hemodynamic level. Comprehensive training across four pillars of fitness yields significant improvements in aerobic fitness, strength, flexibility, and parent-reported mindset scores for pediatric CHD patients, regardless of patient characteristics, diagnosis type, or severity of hemodynamic limitation. Further study is warranted into optimal standardization of training and whether a comprehensive approach amplifies individual pillars to create more than the sum of its parts.