Allogeneic hematopoietic stem cell transplantation (HSCT) is associated with long-term sequelae such as reduced exercise capacity, but whether some degree of spontaneous recovery occurs during childhood is yet to be determined. This prospective multicenter study aimed to evaluate exercise capacity at 1 and 3 years after HSCT. Forty-four (30 males, median age [interquartile] 13.0 years [10.5; 15.4] at first cardiopulmonary exercise test [CPET]) of the 292 children included in the RESPPEDHEM cohort had a CPET at both time points. Their median z-score of peak V'O did not significantly improve between the two CPETs: -2.7 (-4.0; -1.5) at 1 year versus -2.2 (-3.1; -0.6) at 3 years, p = 0.09. It was associated with a low z-score of peak oxygen pulse: -2.2 (-3.6; -0.9) versus -1.9 (-2.8; -0.9), p = 0.14, suggesting low muscular fitness. Female sex was associated with a higher risk of low muscular fitness, whereas the Play-Performance Scale (PPS) was unable to differentiate between adolescents with or without low fitness (37/39 adolescents had a PPS score evaluated by their parents of 100 and were judged as fully active and normal, contrasting with the results of their CPET). In conclusion, impaired exercise capacity is present one1 year after HSCT, does not improve after two subsequent years in adolescents, and is under-evaluated by their parents. CLINICALTRIALS.GOV IDENTIFIER: NCT02032381.