The purpose of this study was to understand why adolescents choose to eat fewer fruits and vegetables by examining the stages of behavioral change and perceived barriers to fruits and vegetable intake in a school-based study in Japan. A cross-sectional survey was performed at junior and senior high schools from 2018 to 2020, and 933 students aged 12–18 agreed to participate. A questionnaire obtained information on demographic characteristics,
daily fruit and vegetable intake, and to assess the stage of change regarding eating more fruits and vegetables and barriers faced by the participants. The daily average amount of fruit and vegetable intake was 89.3 g and 178 g, respectively. In response to whether they were “Eating 350 g or more vegetables and 200 g or more fruits a day most day,” 52.6% answered “not thinking about doing it” (precontemplation stage); the ratio was particularly high among males (61.1%). Moreover, as the stage of change increased from precontemplation to action/maintenance, the daily intake of fruits and vegetables increased and the perceived barriers decreased. We also found that environment when dining out, personal habits, and family and self-preference were perceived as the most important factors related to barriers to eating more fruits and vegetables. This study suggests that stage-tailored interventions need to target the above-mentioned barriers, particularly for students in the precontemplation and contemplation stages, and to enhance knowledge on the health benefits of fruits and vegetables, as well as consider a gender-specific approach.