Autonomic nervous imbalance is implicated in chronic headache. We investigated the effects of goshuyuto-a representative Kampo medicine for headache-on the lateralization of the pupillary autonomic nervous system by using binocular infrared video pupillography. Patients with chronic headache were administered goshuyuto extract for 1 month (1st stage). Goshuyuto was discontinued for 1 month, following which the patients were randomly divided into 2 groups: placebo and goshuyuto. In the 2nd stage, the respective groups were administered placebo or goshuyuto for 3 months. The average laterality of the pupillary dynamics decreased significantly in the goshuyuto group. These results suggest that the reduction of the difference in pupillary autonomic balance between the left and right eyes might be one of the action mechanisms of goshuyuto to relieve chronic headache.