We investigated the effects of pulsed magnetic fields (PMF) stimulus on electroencephalogram (EEG) alpha activity and heart rate variability (HRV) from electrocardiogram (ECG) measurements with various stimulus durations at acupoint PC9. The alpha activity in the EEG and the ratio of low frequency power and high frequency power (LHR) in the HRV, a reflection of sympathovagal activity, were increased and decreased, respectively, after PMF stimulus of 3 min. Our spectral analysis quantitatively proved that the changes in the EEG alpha activity were consistent with an autonomic function in the ECG. These findings suggest that appropriate PMF stimulus results in the same effect as that of acupuncture applied to the acupoint PC9, which is closely related to the parasympathetic activity of the autonomic nervous system.