Type 1 diabetes is commonly associated with autonomic neuropathy. The present study investigated the influences of glycemic control, disease duration (DD), and exercise on autonomic nervous function in children with type 1 diabetes by analysis of their heart rate variability (HRV). Methods: Seventy-nine type 1 diabetic children were recruited and categorized into four groups by HbA1c of 8% and DD of 4.5 years. HRV parameters as determined by separate frequency domain components (low frequency: LnLF, 0.04–0.15 Hz; high frequency: LnHF, 0.15–0.5 Hz; total power: LnTP, 0.04–0.5 Hz) were measured both at rest and during exercise. Pearson's correlation, one-way ANOVA, and multiple regressions with stepwise method were used for statistical analysis. Results: While at rest, HbA1c and DD were negatively correlated with all HRV parameters. Both HbA1c and DD were significant predictors in LnTP. However, only HbA1c was a significant predictor in LnLF and LnHF. Type 1 diabetes patients with HbA1c > 8% and DD > 4.5 years had a significantly lower HRV than the other patients. During exercise, HRV reduced significantly and no significant correlation between HbA1c and HRV or between DD and HRV was observed. Also, a significant difference in HRV among the four groups was not demonstrated. The smallest decrement in HRV from resting to exercise were in subjects with HbA1c > 8% and DD > 4.5 years. Conclusion: HbA1c was a more dominant predictor for LnTP, LnHF and LnLF than DD in children with type 1 diabetes at rest. HRV reduced significantly from resting to exercise. However, the responses of HRV during exercise differ from the responses of HRV at rest.