Background: The aim of this study was to assess within-breath respiratory system impedance by the forced oscillation technique (FOT) in children with cystic fibrosis (CF) and relate it to the underlying lung disease. Methods: Thirty-three children with CF (median [range] age 12.0 [6-17] years) underwent FOT at 8 Hz during tidal breathing, multiple breath nitrogen washout (LCI), spirometry (FEV1), body plethysmography (RV/TLC), and magnetic resonance imaging (MRI). FOT outcomes included: mean inspiratory, expiratory, and whole breath resistance (R8INSP, R8EXP, R8TOT) and reactance (X8INSP, X8EXP, X8TOT), and the differences between X8INSP and X8EXP (ΔX8). Morphological changes were evaluated by MRI using CF-specific morphological scores. Spearman correlation was performed to examine the correlation between FOT indices and other parameters. Results: FEV1 was negatively correlated with R8EXP (r = −0.52, P = 0.002) and ΔX8 (r = −0.55, P = 0.001), and positively correlated with and X8EXP (r = 0.56, P < 0.001). RV/TLC was positively correlated with R8EXP (r = 0.43, P = 0.013), and ΔX8 (r = 0.54, P = 0.001) and negatively correlated with X8EXP (r = −0.54, P = 0.001). We found poor correlation between FOT parameters and LCI and no correlation between FOT parameters and MRI scores. Conclusion: In children with CF, changes in within-breath FOT parameters are consistent with peripheral obstruction and dynamic airway compression, while they are not associated with ventilation heterogeneities and morphological alterations.