Little is known about motor competence and the longitudinal development of motor performance among youth with cystic fibrosis (CF). In this study, we assessed aspects of motor performance in different age groups of young patients with CF and compared them with a healthy reference group of same aged children. We also examined the development of motor performance among different age groups of these children with CF, using The Deutscher Motorik Test (DMT) to assess attributes of health-related and motor performance-related fitness. We used an incremental ergometer cycle test to determine maximal exercise capacity (expressed as peak workload). We evaluated and recorded habitual physical activity (PA) as measured by the number of steps per day and the time spent in different PA intensities (expressed in metabolic equivalents). In total, 31 children and adolescents with CF agreed to participate (13 girls,18 boys) aged 6–17 years ( M  = 11.3, SD =3.3 years); they had a mean one second forced expiratory volume (expressed as a percentage of predicted value [% pred]) of 87.2% ( SD = 22.3%). We found their values of health-related and motor performance-related fitness to be significantly lower ( p  < 0.05) than those of their healthy peer participants. In contrast to the reference group, participants with CF up to 14 years of age showed a linear improvement in these values and in their PA, followed by a plateau or even a nonsignificant decrease after age 14. These findings have important implications for the development and prescription of exercise programs for children with CF. Besides aerobic and strength exercises, we recommend that neuromuscular training be integrated into exercise programs to improve the coordinative abilities of youth with CF. More attention should be paid to vulnerable older adolescents to ensure their long-term motivation to maintain exercise participation.