Sensory gating is a preattentional mechanism to filter irrelevant information from the environment. It is typically reflected as a suppression of the event-related P50 component for successive sounds in the auditory modality. Although stress-induced sympathetic activation has been reported to disrupt P50 suppression, little is known about the modulatory effect of parasympathetic activation on early auditory sensory gating. We determined the parasympathetic effect on the magnetic P50 (P50m) suppression by controlling the respiratory rhythm and recording data simultaneously with magnetoencephalography and electrocardiography, using three successive click sounds as stimulus and ten normal individuals as study participants. The respiratory rhythm was guided by visual cues and set at 0.3, 0.25, or 0.2 Hz for distinct auditory stimulus sequence blocks. Heart rate variability analysis showed that slow respiration leads to significantly large high-frequency power, which is known as the parasympathetic index, whereas low-frequency/high-frequency ratio, known as the sympathetic index, did not differ with the respiratory rhythm. Although P50m suppression was observed in the left and right primary auditory areas for every respiratory condition, the left P50m intensity for the first sound was significantly decreased in the case of slow respiration, thereby indicating disruption of the left P50m suppression. Since background alpha oscillatory power, reflecting the arousal level, was similar for every respiratory rhythm, it is concluded that parasympathetic activation enhanced by slow respiration modulates P50m gating by reducing the initial neural sensitivity for an auditory input. Not only sympathetic but also parasympathetic effects should be considered in the evaluation of P50/P50m biomarkers.