Exercise is beneficial for patients with cystic fibrosis (CF) but long-term effects of physical activity on lung function evolution are unknown. We evaluated the longitudinal relationship between changes in habitual physical activity (HPA) and rate of decline in lung function in patients with CF. We tracked HPA using the Habitual Activity Estimation Scale, forced expiratory volume in 1 s (FEV₁) and Stage I exercise tests in 212 patients with CF over a 9-year period. Adjusting for sex, baseline age and FEV₁, mucoid Pseudomonas aeruginosa and CF-related diabetes, mean ± sd FEV₁ % predicted decreased by 1.63 ± 0.08% per year (p<0.0001) while mean ± sd HPA increased by 0.28 ± 0.03 h·day(-1) per year (p<0.0001) over the study period. A greater increase in HPA was associated with a slower rate of decline in FEV₁ (r=0.19, p<0.0069). Dividing subjects into "high" and "low" activity (above or below the mean rate of change of activity, respectively), a steeper rate of FEV₁ decline was observed for low (-1.90% per year) compared to high (-1.39% per year) (p=0.002). Increases in HPA are feasible despite progression of lung disease and are associated with a slower rate of decline in FEV₁, highlighting the benefit of regular physical activity, and its positive impact on lung function in patients with CF.