Massotherapy, the therapeutic use of massage, is used to treat various chronic pain syndromes. One type of massotherapy, pressure stimulus applied over trigger points (TPs), is reported to have excellent therapeutic effects. Its effect is possibly mediated through changes in the autonomic nervous system although little research has been conducted to assess autonomic activity during TP compression. We have investigated how compression applied over TPs affects the autonomic nervous system. Six healthy young adult females whose daily working routine was carried out predominantly in a standing position were enrolled in the study cohort. After a day's work, the subjects were asked to rest supine, and electrocardiograms (ECGs), instantaneous lung volume (ILV) and systolic and diastolic blood pressures (SBP, DBP) were measured before and after pressure application over the TPs in those lower limb muscles where the subjects felt muscle fatigue or discomfort. The subjects were also asked to coordinate breathing with the beeping sounds. The therapeutic effects of TP compression were assessed by a subjective fatigue scale. Parasympathetic nervous activity was also assessed by spectral analysis of heart rate (HR) variability. The transfer function from ILV to HR was evaluated using linear analysis. The results indicated that TP compression (1) decreased HR, SBP and DBP, (2) increased parasympathetic activity, (3) increased the gain from ILV to HR, and (4) improved the fatigue scores. These findings suggest that an increase in parasympathetic nervous activity after the TP compression induced a reduction of fatigue. The therapeutic mechanisms of TP compression to enhance parasympathetic nervous system are discussed.