Background: Autonomic nervous system balance is altered in cystic fibrosis (CF), although its influence on physical fitness has been poorly explored. Objective: This study aimed to evaluate the association of heart rate variability (HRV) with exercise capacity and levels of daily physical activity in children and adolescents with mild-to-moderate CF. Methods: A cross-sectional study including individuals with CF aged 6-18 years, not under CFTR modulator therapy, was performed. Sociodernographic (age, sex) and clinical information (airway colonization, pancreatic insufficiency, and genotyping) were collected. In addition, exercise capacity (modified shuttle test - MST), lung function (spirometry), body composition (bioimpedance), levels of daily physical activity (5-day accelerometer), and IIRV (both at rest and during the MST) were evaluated. Results: 30 individuals (20 females) aged 11.2 +/- 3.7 years, mean FEV1 62.8 +/- 27.6%, were included. A synipathovagal balance (LF/HF) increase (p < 0.001) during the MST was shown, indicating a predominance of sympathetic modulation. The standard deviation of all RR intervals (SDNN) and the high frequency (IIF) index during exercise correlated significantly with FIN I (r 0.45, p = 0.01 and r = 0.46, p 0.01; respectively). MST distance also correlated positively and significantly with SDNN (r = 0.13, p = 0.01), square root of the mean of the sums of squares of frequencies between intervals greater than 50 ins - RMSSD (r = 0.53, p < 0.01), low frequency - LF (r = 0.18, p < 0.01), HF (r = 0.64, p < 0.01), dispersion of points perpendicular to the short-term identity line - SD1 (r = 0.40, p = 0.02) and negatively with LF/HF (r = -0.57, p < 0.01). Regarding daily physical activity, SDNN at rest (r = 0.37, p = 0.04) and exercise (r = 0.41, p = 0.02) showed positive correlations with time in moderate-to-vigorous activities. When normalizing the SDNN and classifying individuals as normal or altered, those presenting altered SDNN showed poorest FEV1 (p = 0.001) and lower exercise capacity (p = 0.027). Conclusion: HRV correlates with lung function, exercise capacity and levels of daily physical activity in children and adolescents with CF. The study highlights the influence of CF on autonomic function and suggests HRV measurement as an easy tool to be used m clinical settings as an alternative marker to monitor CF individuals.