BACKGROUND: Breast cancer is one of the leading causes of death worldwide. Heart rate variability (HRV) has attracted scientific community attention in different pathologies, becoming thus an ultimate importance tool in both clinical and research setting, being a good predictor of cardiac events and mortality risk and also used in physical exercise and sports in general. The aim of the present study was to evaluate 12 weeks of exercise training and six weeks of detraining in cardiorespiratory capacity, and autonomic modulation in breast cancer patients. METHODS: The sample was composed of 18 females (9 controls and 9 exercised), (aged 30-60 years). The HRV in the time and frequency domain was performed using an electrocardiogram before, after 12 weeks of the session of exercise training and after six weeks of detraining. Shapiro-Wilk and Mann-Whitney tests were made. RESULTS: No significant changes in time domain were found. In the frequency domain, 12 weeks of exercise training promote a decrease in LF (nu) and decrease in HF (nu) Index. The exercise training period promoted a decrease in LF/HF. The autonomic data returned to baseline levels after the detraining period. However, cardiorespiratory capacity remained increased after the detraining period. CONCLUSIONS: These data demonstrated that exercise training can be used to prevent autonomic dysfunction in breast cancer patients, but detraining promotes loss of all autonomic benefits.