Background and Objectives: Exercise enhances cardiovascular health through various mechanisms, including the modulation of autonomic nervous system activity. This study aimed to systematically examine the impact of exercise on heart rate variability (HRV) in adults during and within one hour after exercise (WHAE). Materials and Methods: A comprehensive literature review was conducted using the MEDLINE, Embase, Cochrane Library, Scopus, and PubMed databases to identify published studies that reported the impact of exercise on autonomic nervous system activity in adults. The studies measured the absolute power of the low-frequency band (0.04-0.15 Hz) to the absolute power of the high-frequency band (0.015-0.4 Hz) (LF/HF ratio) to assess sympathetic activity and the root mean square of successive differences between normal heartbeats (RMSSD) to assess parasympathetic activity. Results: A total of 3329 studies were screened for relevance, and finally, 10 articles that utilized methods for measuring autonomic nervous system activity, such as the LF/HF ratio and RMSSD, covering 292 adult patients, were included for meta-analysis. In the current meta-analysis, we observed a significant decrease in parasympathetic activity during and after exercise, as indicated by RMSSD, compared to pre-exercise levels (mean difference [MD] = -4.96, 95% confidence interval [CI]: -8.00 to -1.91, p = 0.003). However, sympathetic activity after exercise, represented by the LF/HF ratio, showed a borderline significant increase compared to pre-exercise levels (MD = 1.06, 95% CI: -0.01 to 2.12, p = 0.052). The meta-regression model found that factors associated with RMSSD included mean age, male gender, and duration post-exercise. Additionally, the factor associated with the LF/HF ratio was the healthy condition of participants. The trial sequential analysis provided robust evidence of a decrease in RMSSD and an increase in the LF/HF ratio during and WHAE. Conclusions: Given the limitations of the current study, the findings suggest that a significant decrease in parasympathetic activity and a borderline significant increase in sympathetic activity in adults during and WHAE, as confirmed by trial sequential analysis. Meta-regression analysis indicated that parasympathetic activity was negatively associated with participant age and male gender, but positively associated with duration post-exercise. Additionally, increased sympathetic activity was linked to the healthy conditions of participants. This study suggests that exercise might differentially affect autonomic balance in individuals with chronic conditions compared to healthy individuals. This highlights the potential need for tailored exercise interventions to improve autonomic function across different populations.