Food waste globally affects food security and sustainability. There currently are few studies focusing on food waste in schools. The present study aimed to determine the meal quality and plate waste in school lunch programme in Thailand. This cross-sectional study was conducted in canteens of representing kindergarten and elementary schools in Southern Thailand within their real-life context. The assessment was carried out over five consecutive school days in July–August 2020 for each school, at which two types of menus, including rice with side dish and one-dish meal were served. Waste collection and quantification were conducted by selective aggregate weighing, according to the Food Loss and Waste Protocol. All lunch menus contained excess rice but insufficient meats, fruits, vegetables and eggs, regarding the national lunch standard. For each serving portion, 7–33 % rice, 9–22 % meats, 7–65 % vegetables, 1–19 % fruits and 3–14 % eggs were discarded. Plate waste from rice with side dish menus (10–29 %) was more than one-dish meals (7–17 %). By estimation, each kindergartener generated 71⋅4 g plate waste daily, accounting for the caloric and monetary values of 146 kcal and 0⋅16 US dollar. The amount of plate waste and the respective caloric and monetary losses were less obvious at the elementary school. Plate waste affected the adequacy of food intakes of schoolchildren from lunch meals. The data obtained from the present study will be useful for planning and implementation of school lunch programme in Thailand and countries with similar context.