Multiple chemical sensitivity (MCS) onset in minors can greatly impact learning and future employment. This study investigated the prevalence of MCS and related factors in high school students to determine whether it was the same as in adults. A comprehensive survey was conducted on 80 high schools in Gunma Prefecture, Japan. The survey incorporated the Quick Environmental Exposure and Sensitivity Inventory, as well as items related to allergies, the living environment, and lifestyle. Of the 4630 students analyzed, according to Hojo's cut-off value, 9.0% were classified as high-risk for MCS and 77.9% reported some allergy-like symptoms. Significant factors associated with elevated MCS risk included female sex, having various allergic conditions, having experienced living in a new home or home renovations or extensions, proximity to environmental stressors (freeways, national highway, factories, rubbish dumps, or sources of offensive odors), insufficient physical activity (exercising less than once a week outside of physical education classes), having cold hands and feet, being fatigued, having a bedtime earlier than 11 p.m., and having moderate-frequent subjective stress. Overall, 9.0% of high school students in Japan are at high risk for MCS. Enhancing awareness of MCS-like symptoms and addressing allergies, living environments, and lifestyle habits may mitigate these symptoms.