OBJECTIVE The role of school lunches in diet quality has not been well studied. Here, we aimed to determine the contribution of school lunches to overall nutrient intake in Japanese schoolchildren. METHODS The study was conducted nationwide under a cross-sectional design. A non-consecutive, three-day diet record was performed on two school days and a non-school day separately. The prevalence of inadequate nutrient intake was estimated for intakes on one of the school days and the non-school day, and for daily habitual intake estimated by the best-power method. The relationship between food intake and nutrient intake adequacy was examined. METHODS Fourteen elementary and thirteen junior high schools in Japan. METHODS Elementary-school children (n 629) and junior high-school children (n 281). RESULTS Intakes between the school and non-school days were significantly different for ≥60 % of nutrients. Almost all inadequacies were more prevalent on the non-school day. Regarding habitual intake, a high prevalence of inadequacy was observed for fat (29·9-47·7 %), dietary fibre (18·1-76·1 %) and salt (97·0-100 %). Inadequate habitual intake of vitamins and minerals (except Na) was infrequent in elementary-school children, but was observed in junior high-school children, particularly boys. CONCLUSIONS School lunches appear to improve total diet quality, particularly intake of most vitamins and minerals in Japanese children. However, excess intakes of fat and salt and insufficient intake of dietary fibre were major problems in this population. The contribution of school lunches to improving the intakes of these three nutrients was considered insufficient.