AbstractTransient global amnesia (TGA) often involves precipitating events associated with changes in autonomic nervous system (ANS), and heart rate variability (HRV) reflects the ANS state. This study aimed to investigate HRV changes after TGA. A retrospective analysis of HRV included patients diagnosed with TGA between January 2015 and May 2020. The time and frequency domains of HRV were compared among three groups: early (< 1 week after TGA, n = 19), late (1–4 weeks after TGA, n = 38), and healthy control (HC, n = 19). The Pearson’s correlation between time and time-domain HRV was also examined. The standard deviation of NN intervals (SD_NN) (early, 47.2; late, 35.5; HC, 41.5; p = 0.033) and root mean square of successive RR interval differences (RMSSD) (early, 38.5; late, 21.3; HC, 31.0; p = 0.006) differed significantly among the three groups. Post-hoc analysis showed statistically significant differences only in the early and late groups in both SDNN (p = 0.032) and RMSSD (p = 0.006) values. However, the frequency domain with total power, low-frequency and high-frequency powers, and low-frequency/high-frequency ratio did not differ. SD_NN (Pearson correlation coefficient =− 0.396, p = 0.002) and RMSSD (Pearson correlation coefficient =− 0.406, p = 0.002) were negatively correlated with time after TGA. Changes in HRV occurred over time after the onset of TGA, with the pattern showing an increase in the first week and then a decrease within 4 weeks.