Background: The effects of the odors of natural essential oils on humans are divided into psychological and physiological effects, such as alertness and sedative effects, respectively. However, there are only a few studies on the effects of essential oils derived from materials specific to Japan. In this study, we focused on Japanese citrus fruits and determined the effects of essential oil aromas on human physiology and psychology.Methods: A total of 16 men and 16 women (aged, 20–24 years) participated in this study. Essential oils of the Japanese citrus iyokan (Citrus iyo) and yuzu (Citrus junos) were used as tests with the essential oils of Valencia orange (Citrus sinensis Valencia) used for comparison. Each essential oil was soaked in cotton and placed at the bottom of a vial and presented to the participant’s nose in a blind manner. The control was to breathe clean air for 2 min; the condition that inhaled the vapor of each essential oil for 2 min was compared to the control. Autonomic nervous activity was evaluated using the pupillary light reflex and fingertip temperature measurements; central nervous activity was assessed by near-infrared spectroscopy. The mood and emotion changes before and after inhalation of each odor of the essential oils were examined using a visual analog scale and multiple mood scales.Results: The inhalation of essential oils from Japanese citrus fruits significantly increased miosis rate and fingertip temperature. Cerebral blood flow in the prefrontal area significantly increased. Subjectively, the feeling of fatigue was reduced, and the feeling of refreshment and concentration improved.Conclusions: Predominance of parasympathetic nerve activity was led by suppression of sympathetic nerve activity, suggesting that inhalation of essential oils from Japanese citrus fruits has a sedative effect on the body. Conversely, the cerebrum was activated due to an increase in cerebral blood flow. The reduction of fatigue and improvement of concentration observed in the subjective evaluation might be caused by the sedative effect on the body and the activation of the cerebrum.Trial registration: The trial registration number (TRN) is UMIN-CTR, UMIN000032773 and date of registration is May 30, 2018 (https://upload.umin.ac.jp/cgi-open-bin/ctr/ctr_view.cgi?recptno=R000037389).