Background: The aim of this study was to investigate the effects of a monitored exercise program on aerobic fitness in children with cystic fibrosis (CF). Methods: Six children (2f/4m) with ages ranging from 6 to 14 years (11.3 ± 3.3 years.) and a mean ppFEV1 102.5 ± 13.5% pred. participated in the partially monitored 12-month exercise program. VO2peak and Wpeak were used as parameters of aerobic fitness. Incremental Cardio-Pulmonary Exercise Tests (CPETs) were performed before the program began (T1), after 6 months (T3) of monitoring, and after a further 6 months (T4) without monitoring. Habitual physical activity (HPA) was assessed with accelerometry. Results: The values of VO2peak and Wpeak improved slightly from T1 to T3 (p > 0.05), without a further increase after monitoring was stopped (T4). However, the VO2peak and Wpeak values were higher after monitoring was stopped compared to at T1. The exercise program with and without monitoring (p > 0.05) had no or only a slight effect on the FEV1 values, steps/day, and the intensity of HPA. Conclusions: Monitoring seems to facilitate the achievement of beneficial effects on physical fitness in CF children. For that reason, continuous individual exercise monitoring programs that involve close contact with an exercise therapist should be provided to maintain long-term motivation and participation in physical activities and sport activities during leisure time.