Background Cystic fibrosis (CF) lung disease begins early in life and progresses throughout childhood into adolescence. Children completing the Australasian CF Bronchoalveolar Lavage (ACFBAL) trial were followed longitudinally (CF-FAB study) to determine progression of CF lung disease during adolescence using visual and automatic methods and to correlate CT-derived metrics with spirometry outcomes. Methods CTs from start and end visits of CF-FAB (mean 24 [SD 12] months apart) were analysed using visual PRAGMA-CF scoring and automatic bronchus-artery (BA) analysis. PRAGMA-CF assessed %Disease by summing %Bronchiectasis, %Mucus plugging, % Airway wall thickening on inspiratory scans and %Trapped air on expiratory scans. The BA-analysis segments the bronchial tree, identifies segmental bronchi (G0) and distal generations (G1, G2, G3…), measures diameters of bronchial outer wall (Bout), inner wall (Bin), wall thickness (Bwt), and artery (A), and computes BA-ratios (Bout/A, Bin/A, Bwt/A, Bwa/Boa[=bronchial wall area/bronchial outer area]) to evaluate bronchial dilatation and wall thickening. Results 120 children (median age 13 years, IQR 11.4-14) contributed 115 start and 105 end scans. Eleven children were treated with CFTR modulators prior to the start of the study and four received the treatment during the study. Progression was found in PRAGMA-CF %Bronchiectasis (p=0.02) and %Mucus plugging (p=0.02), and Bout/A (p=0.01), Bwt/A (p<0.001), and Bwa/Boa (p<0.001). Spirometry outcomes showed no significant decline. BA-metrics correlated more strongly with spirometry outcomes than PRAGMA-CF scores. Conclusion Heterogeneous progression of structural lung disease in children with CF during adolescence was detected using visual PRAGMA-CF scores and automatic BA-analysis. Spirometry outcomes showed no significant decline.