Little is known about the effects of the non-cognitive skills on health. In this study, questionnaires were distributed to 1,658 school children aged 6–16 years and their parents in Hyogo Prefecture in Japan, who completed them at home and returned them in Freepost envelopes. The questionnaires included items about the child and his/her self-rated health (SRH), lifestyle, food-related habits and attitudes. The responses were anonymous and unidentifiable. Associations between the independent variables and high/low non-cognitive skills were assessed with the χ2 test or Fisher’s exact test at a 5% level of significance. Groups with high and low non-cognitive skills were defined and factors that differed significantly between them were examined using logistic regression analysis. In total, 496 (29.9%) returned both completed questionnaires. In this study, we separated the children and students aged 6–12 and 13–16 years, respectively. Furthermore, we categorized them according to the Japanese education system. Among the children aged 6–12 years, the high non-cognitive skills group suffered fewer headaches, went to bed earlier, had a greater preference for home-cooked meals, and had better exercise habits compared with the low non-cognitive skills group. In the students aged 13–16 years, the high non-cognitive skills group experienced fewer headaches, went to bed earlier, had a greater preference for home-cooked meals, and had better exercise habits compared with the low non-cognitive skills group. In conclusion, the findings of this study suggested that a high level of non-cognitive skills was associated with high SRH and greater concern about food.