Japan is facing a markedly high incidence of adolescent suicide. This study examines the relationship between depression and self-rated health, which is a significant factor driving people towards suicide, highlighting the importance of children’s assessments of their health. In this cross-sectional study, an original questionnaire combining text and illustrations was administered to 6421 elementary, junior, and senior high-school students and an effective way of using the questionnaire was proposed. To assess children’s self-rated health, the survey questions were classified into two domains: physical and mental health. The questions were further classified based on symptom duration. Depression assessment was based on the Depression Self-Rating Scale for Children. To provide a basis for the effective use of the self-rated health assessment tool, the respondents were classified into three groups based on physical/mental conditions together with the duration of those conditions, and comparisons were subsequently made. The groups were Favourable Health, Temporarily Poor Health, and Persistently Poor Health, and the results were analysed using an ANOVA. Self-rated health levels decreased, and depressive conditions worsened with age. Although most children led physically and mentally healthy school lives, the mean Depression Self-Rating Scale score was significantly higher for the Persistently Poor Health group than the other two, and the Temporarily Poor Health group scored significantly higher than the Favourable Health group for both physical and mental health (all p < 0.001). As the Temporarily and Persistently Poor Health groups in the domains of physical and mental health are more likely to be depressed, it is important to monitor the health of children in educational settings. In this study, completing this questionnaire was shown to help children understand themselves objectively and help the adults around them comprehend their condition quicker. It is especially important to promptly develop systems for appropriate and organic collaboration between educational settings and medical or welfare services.