The well-being of young people-particularly aspects such as physical and mental health-has become an increasing concern for Japan's government due, in part, to the aging and declining depopulation that Japan has been experiencing in recent years. Considering this, a survey of well-being and travel-to-school behavior was carried out in four high schools of Hiroshima Prefecture, Japan; between May and September 2016 with 1,017 valid samples. The respondents' ages vary between 15 and 19 years old. We argue that transport-based social exclusion results from not only situations of transport disadvantage, but also reduced or deteriorated individual well-being. Here, well-being is measured by using constructs grouped into three main categories: happiness, healthy lifestyle propensity, and social exclusion. We found the following potential issues of transport-based social exclusion: residents in depopulating areas experience lower levels of well-being than people in non-depopulating areas. Travel times longer than 30 minutes have negative effects on happiness, traffic safety perception, health conditions, and personal health habits. Bicycle users tend to experience higher levels of wellbeing in general, whereas bus and car users tend to experience less in comparison. Special attention should be paid to improving affordability and flexibility of bus services for students.