Objective To systematically review the effect of percutaneous acupoint electrical stimulation (TEAS) on heart rate variability (HRV). Methods The PubMed, Embase, Ovid MEDLINE, Cochrane Library, CNKI, WanFang Data, VIP, and CBM databases were electronically searched to collect randomized controlled trials (RCTs) on the effects of percutaneous acupoint electrical stimulation on heart rate variability from inception to February 28, 2023. Two reviewers independently screened the literature, extracted data, and assessed the risk of bias of the included studies. Meta-analysis was then performed using RevMan 5.4 software. Results A total of 14 RCTs involving 719 patients were included. The results of meta-analysis showed that SDNN (MD=12.95, 95%CI 9.18 to 16.72, P<0.01), RMSSD (MD=1.81, 95%CI 0.10 to 3.53, P=0.04), pNN50 (MD=1.75, 95%CI 1.02 to 2.48, P<0.01), HF (SMD=0.27, 95%CI 0.01 to 0.52, P=0.04), LF/HF (MD=−0.07, 95%CI −0.12 to −0.03, P<0.01), ln-LF (MD=0.63, 95%CI 0.25 to 1.01, P<0.01), ln-HF (MD=1.05, 95%CI 0.60 to 1.49, P<0.01), mean RR (MD=−11.86, 95%CI −21.77 to −1.96, P=0.02), and HR (SMD=−0.43, 95%CI −0.66 to −0.20, P<0.01) all showed improvement compared with the control group. However, there were no significant differences between the two groups in LF (SMD=0.15, 95%CI −0.10 to 0.40, P=0.23), LF norm (SMD=0.24, 95%CI −0.10 to 0.58, P=0.16) or HF norm (SMD=0.25, 95%CI −0.47 to 0.97, P=0.5). TEAS on PC6: SDNN, pNN50, HF, LF/HF, LF norm, HF norm, ln-LF, ln-HF, and HR all showed improvement compared with the control group. However, there were no significant differences between the two groups in RMSSD, LF, or RR interval. Conclusion This study supports the improvement of heart rate variability by transcutaneous acupoint electrical stimulation and PC6 acupoint selection. Due to the limited quantity and quality of the included studies, more high-quality studies are needed to verify the above conclusion.