Dietary supplements can be used to compensate for an inadequate diet. However, some studies indicate that supplement users consume healthier diets than non-users, although such data are lacking in Japanese children. The aim of the present study was to investigate the food and nutrient intake of dietary supplement users among school-aged children in Japan. A nationwide school dietary survey was conducted at fourteen elementary schools and thirteen junior high schools in twelve prefectures in Japan. Three-day non-consecutive semi-weighed dietary records were obtained on two weekdays and one weekend day. Analysis of covariance was performed to investigate differences in food and nutrient intake from meals consumed at school and outside of school between dietary supplement users and non-users, adjusted for socio-demographic and health-related characteristics. Of the 910 children included in this analysis, 80 (8⋅8 %) reported supplement use. Based on 3-d dietary records, dietary supplement users consumed higher mean amounts of oils and lower amounts of fruits and vegetables than non-users. In school lunches, users consumed significantly higher amounts of oils and lower amounts of protein than non-users. In meals consumed outside of school, dietary supplement users consumed significantly higher amounts of confectioneries and lower amounts of fruits and vegetables, folate, vitamin C and dietary fibre than non-users. Collectively, our findings indicate that dietary supplement users consumed less healthy diets than non-users. Additional studies are warranted to confirm these results and identify factors contributing to poorer dietary habits in supplement users.