Adverse cardiovascular events and increased mortality are associated with cardiac autonomic nervous system dysfunction in the early stages of the systemic sclerosis (SSc), even prior to the development of cardiac fibrosis. The objective of the study was to evaluate the impact of a three-month exercise training regimen and a subsequent comparable period of detraining on the activity of the cardiac autonomic nervous system in patients with SSc. A total of forty patients with SSc were randomized to either the control group (Group COΝ) or the exercise training group (Group ET). Cardiopulmonary exercise testing was performed at baseline, three months later, and six months later to assess peak oxygen uptake (VOpeak). They also had 24 h electrocardiogram monitoring for heart rate variability (HRV) and heart rate turbulence analysis. The following time-domain indices were evaluated in the context of HRV analysis: the standard deviation of NN intervals (SDNN), the root mean square of successive RR interval differences (rMSSD), and the percentage of successive RR intervals that differ by more than 50 ms (pNN50). Additionally, regarding the frequency-domain indicators, the low-frequency (LF) and high-frequency (HF) components, as well as the LF/HF ratio, were evaluated. Independent -tests and Chi-square tests were used for baseline comparisons, while two-way repeated measures ANOVA with Bonferroni post hoc tests assessed changes over time and between groups. Linear and multiple regression analyses were conducted to explore relationships among variables and identify predictors of HRV indices and VOpeak. Group ET implemented a three-month mixed-type exercise training program, while Group COΝ received standard care. Group ET improved indices of vagal activity [rMSSD by 32.6% ( = 0.017), pNN50 by 57.1% ( = 0.01) and HF by 20.1% ( = 0.01)] and sympathovagal activity [SDNN by 15.5% ( = 0.002) and LF/HF by 12.03% ( = 0.004)] after three months. Exercising patients also increased their VOpeak by 20.8% ( = 0.001). A robust positive correlation was observed between ΔVOpeak and ΔSDNN (r = 0.754, < 0.001). After three months, there was no statistically significant difference in the VOpeak or any HRV index in the group COΝ. Compared to the baseline values, there was no statistically significant difference in group ET at 6 months, whereas the control group exhibited a decline. In summary, a three-month mixed-type exercise training program can enhance the cardiorespiratory efficiency and cardiac autonomic nervous system function of patients with SSc, as well as alleviate the deterioration that arises following the detraining period.