Dental treatment uses materials such as resin that emit unpleasant volatile odors. These odors have been suggested to cause emotional distress and vomiting in patients, leading to the negative recall of dental treatments due to their smell. This study aimed to evaluate brain correlates of the stress response when sniffing the odor of dental treatment materials. Using functional near infrared spectroscopy (fNIRS) and a visual analog scale (VAS) of odor unpleasantness, we evaluated the degree of discomfort in 18 healthy subjects when sniffing resin odor. We measured the activity of the prefrontal cortex when subjects sniffed resin and used a T&T Olfactometer (Daiichi Yakuhin Sangyo. Ltd) to generate C-5 (unpleasant) and D-5 (pleasant) odors. The VAS and fNIRS activity level in the prefrontal cortex were C5>resin>D5 in magnitude. Thus, there was a tendency for prefrontal cortex activity to register the strength of unpleasantness of odors, including those emitted in dental procedures. We conclude that odors used in dental treatment elicit a stress-associated neural response. Therefore, odor protection in dental clinics is important for relieving the stress of patients under treatment.