BACKGROUND: To evaluate the influence of functional training on the geometric indices of heart rate variability (HRV) and fractal correlation properties of the dynamics of heart rate in menopausal women. METHODS: Of 39 women who were in the period of menopause for more than a year and who did not practice any regular physical activity were divided into: Functional training group (FTG = 50 +/- 4.5 years; 67.64 +/- 11.64 kg; 1.5 +/- 0.05 m) that executed the functional training (FT) and all proposals by reviews and the Control group (58.45 +/- 4.8 years; 66.91 +/- 13.24 kg; 1.55 +/- 0.05 m) who performed all assessments but not FT. The training consisted of 18 weeks (three times a week) and the volunteers performed three sets of 11 functional exercises followed by a walk in each of the sessions. The autonomic nervous system modulation was evaluated by analysis of HRV and the indices obtained were: RR intervals, RRTRI, TINN, SD1, SD2, SD1/SD2, qualitative analysis of Poincare plot and DFA (alfa-1, alfa-2 and alfa-1/alfa-2). The Student\'s t-test for unpaired samples (normal data) or Mann-Whitney test nonnormal data) were used to compare the differences obtained between the final moment and the initial moment of the studied groups (p < .05). CONCLUSION: Were observed in the FTG: increased SD1 (CG 0.13 +/- 4.00 vs. 3.60 +/- 8.43), beat-to-beat global dispersion much greater as an increased in the dispersion of long-term RR intervals and increased fractal properties of short-term (alpha1) (CG -0.04 +/- 0.13 vs. 0.07 +/- 0.21). FT promoted a beneficial impact on cardiac autonomic modulation, characterized by increased parasympathetic activity and short-term fractal properties of the dynamics of the heart rate.