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Introduction: Cardiovascular adaptation in pregnancy is the most important changes related to aerobic training. Heart rate variability is one of the most important cardiovascular health parameters. Pregnancy and training as a kind of stress affect cardiovascular system. However, appropriate research regarding this issue is not enough. Therefore, this study was performed with aim to evaluate the effect of aerobic training on heart rate variability in pregnant women. Methods: This randomized clinical trial was performed on 22 healthy pregnant women in Shahid Akbarabadi hospital of Tehran in 2019. There were 12 healthy pregnant women with gestational age of 24-26 week in the intervention group and 10 healthy pregnant women in the control group. The intervention group participated in 8 week aerobic training with moderate intensity. Time and frequency parameters of heart rate variability were monitored in pregnant women with electrocardiogram lead two and AST3000 Avicenna software.data were analyzed by SPSS software (version 24) and Mann Whitney U, Wilcoxon, fisher, paired t, independent t, and Shapiro-Wilk tests. P<0.05 was considered statistically significant. Results: Mean of time domain  and low frequency parameters were significantly higher in pregnant women who had trained at 34th week of pregnancy than pregnant women in the control group (p<0.05). While, no significant changes were observed in mean of time domain and low frequency parameters in control group (P>0.05). Conclusion: Aerobic training improves autonomic nervous system and parasympathetic nervous system superiority.