Adolescence is a crucial period for health status formation. Adolescence is the period during which health-related behaviours, such as nutrition-related behaviours and physical activities, are developed. Self-rated health (SRH) assessment during adolescence is strongly associated with general well-being and psychosomatic symptoms. The current study investigated the relationship between SRH and lifestyle, eating habits and attitudes toward food among junior high school students. A total of 438 students aged 13–15 years and their parents in the Hyogo prefecture of Japan participated in this study. Questionnaires were distributed to the students, who attempted them at home with their parents and returned them via Freepost envelopes. The questionnaires comprised the SRH assessment, lifestyle information, an unidentifiable description of the subject and their guardian’s SRH, and 39 parameters regarding food-related habits and attitudes. The χ2 test or Fisher’s exact test were employed to assess any associations between the independent variables and SRH at a 5% level of significance. The differences between the healthy and unhealthy SRH groups were examined for all significant items using a logistic regression analysis after adjusting for sex and age. Of the participants, 188 (42.9%) returned both completed questionnaires. Among the respondents, 53.2% reported feeling very healthy. SRH assessment did not significantly differ with sex, age or school. Eleven parameters were significantly associated with SRH (P < 0.05 by χ2 test). The guardians’ SRH had no association with the students’ SRH. The excellent SRH group had no headaches [odd’s ratio (OR): 1.68; confidence interval (CI): 1.29–2.18], went to bed early [OR: 1.88; CI: 1.17–3.02], liked home-cooked meals to a greater extent [OR: 2.55; CI: 1.54–4.22], and had good exercise habits [OR: 2.98; CI: 1.27–6.99] compared with the very good to poor SRH group. High SRH was strongly associated with going to bed early, not having headaches, liking home-cooked meals, and having good exercise habits among Japanese junior high school students.