To evaluate the effect of preventive aerobic exercise training on sympathovagal function, cardiac function, and DNA repair capacity in a preclinical model of doxorubicin (DOX)-induced cardiomyopathy. Forty male Wistar-Kyoto rats were allocated into four groups (n = 10/group): D (DOX-treated) and C (controls) remained sedentary, and DT (DOX-trained) and CT (control-trained) performed aerobic training 4 days/week, during 4 weeks before exposure to DOX (4 mg/kg/week during 4 weeks) or saline solution. We evaluated cardiac function (echocardiography), hemodynamic and sympathovagal modulation (artery-femoral cannulation), cardiac troponin T levels, and DNA repair capacity (comet assay). Exercise training preserved ejection fraction (D: − 14.44% vs. DT: − 1.05%, p < 0.001), fractional shortening (D: − 8.96% vs. DT: − 0.27%, p = 0.025) and troponin T levels (D: 6.4 ± 3.6 vs. DT: 2.8 ± 1.7 ng/mL, p = 0.010). DOX increased heart rate variability (C: 27.7 ± 7.9 vs. D: 7.5 ± 2.2 ms2, p < 0.001) and induced sympathovagal dysfunction (LF/HF, C: 0.37 ± 0.15 vs. D: 0.15 ± 0.15, p = 0.036) through exacerbation of sympathetic function (LF, C: 0.22 ± 0.01 vs. D: 0.48 ± 0.24 Hz, p = 0.019). Peripheral mononuclear blood cells of DT animals presented lower residual DNA damage (D: 43.4 ± 8.4% vs. DT: 26 ± 3.4%, p = 0.003 after 1 h). Cardioprotective effects of preventive aerobic exercise training are mediated by preservation of sympathovagal function and improvement of DNA repair capacity of peripheral blood mononuclear cells.