Objectives: This study aimed to compare the effects of high frequency electroacupuncture, low frequency electroacupuncture and manual acupuncture on the autonomic nervous system in stroke patients by using a heart rate variability measuring device. Methods: Thirty-nine participants were recruited and each participated in the high frequency electroacupuncture group, low frequency electroacupuncture group, manual acupuncture group and non-acupuncture group. Some participants received needle insertion with 100 Hz stimulation, with 2Hz stimulation and manual stimulation under mental arithmetic stress during 2 sections. Other participants maintained in the supine position without acupuncture under mental arithmetic stress during the 2 sections. Acupuncture needles were directly inserted perpendicularly to the right Liv 3 acupoint followed by delivery of electric pulses to these points for 8 minutes. Heart rate variability was measured 8 minutes before and 16 minutes after acupuncture stimulation by a heart rate variability measuring system. Results: We found a significant elevated HF total power between 1 section and 2 section and between 1 section and 4 section in the non-acupuncture group, between 3 section and 4 section in the 100Hz electroacupuncture group, and between 1 section and 2 section in the manual acupuncture group and with no change in the 2Hz electroacupuncture group. We also found a significant VLF total power between 2 section and 3 section in the 2Hz electroacupuncture group and between 1 section and 4 section and between 2 section and 4 section in the 100Hz electroacupuncture group. All four groups showed no significant differences in other parameters including heart rate mean, low-frequency power, and the ratio of low-frequency power to high-frequency power. Conclusions: This study may be a basis for research about effects of acupuncture and electroacupuncture because the parameters measured, heart rate variability, showed differences according to acupuncture.