PURPOSE: To study the associations of physical activity (PA), sedentary time (ST), and cardiorespiratory fitness (CRF) with heart rate variability (HRV) in children. METHODS: The participants were a population sample of 377 children aged 6-9 years (49% boys). ST, light PA (LPA), moderate PA (MPA), vigorous PA (VPA), and moderate-to-vigorous PA (MVPA), and PA energy expenditure (PAEE) were assessed using a combined heart rate and movement sensor, maximal power output per kilograms of lean body mass as a measure of CRF by maximal cycle ergometer exercise test, and HRV variables (SDNN, RMSSD, LF, and HF) using 5 min resting electrocardiography. Data were analysed by linear regression adjusted for years from peak height velocity. RESULTS: In boys, ST was inversely associated (β = - 0.185 to - 0.146, p ≤ 0.049) and MVPA, VPA, PAEE, and CRF were directly associated (β = 0.147 to 0.320, p ≤ 0.048) with HRV variables. CRF was directly associated with all HRV variables and PAEE was directly associated with RMSSD after mutual adjustment for ST, PAEE, and CRF (β = 0.169 to 0.270, p ≤ 0.046). In girls, ST was inversely associated (β = - 0.382 to - 0.294, p < 0.001) and LPA, MPA, VPA, MVPA, and PAEE were directly associated with HRV variables (β = 0.144 to 0.348, p ≤ 0.049). After mutual adjustment for ST, PAEE, and CRF, only the inverse associations of ST with HRV variables remained statistically significant. CONCLUSIONS: Higher ST and lower PA and CRF were associated with poorer cardiac autonomic nervous system function in children. Lower CRF in boys and higher ST in girls were the strongest correlates of poorer cardiac autonomic function.