Schools are an important food environment to cultivate and promote healthy food choices and practices among children and adolescents. The aim of the present study was to assess the type and quality of food and beverages sold in school canteens in public primary and secondary schools in Kelantan, Malaysia. Eligible schools were randomly selected from the list of all schools and detailed information of all food and beverage items sold in the school canteens were collected during school days. Food and beverages were classified based on food groups derived from the Malaysian Food Dietary Guideline and the Recommended Foods for Healthy Cafeteria Guideline. An assessment of the traffic-light nutrition food-labelling system of the total sugar content in all pre-packaged foods was also undertaken. A total of 568 food items were identified, with secondary school canteens selling a greater proportion of food items than the primary schools (55.5% vs. 44.5%). In terms of the main food groups, grains and cereal products represented the largest food group served (33-36%), followed by beverages (21-25%) and confectionary and sweet foods (12-13%). In contrast, the vegetable and fruit group represented the smallest proportion of food items sold (1-3%). Comparisons between primary and secondary schools showed a similar trend and pattern of food types and quality of foods sold, except for animal-based foods. A greater percentage of food items in this category was found among secondary schools (12.1%) versus primary schools (6.7%). When total sugar content of all pre-packaged foods was quantified based on the traffic-light nutrition-labelling system, almost one-third of foods and beverages were classified as high (29.1%). Confectionary (19.1%) and flavoured milk and fruit drinks (10.0%) both exceeded the recommended sugar levels of >22.5 g per 100 g and >11.25 mL per 100 m L, respectively. Only one of these packaged foods and beverages (0.9%) was classified as a healthy food choice. About a quarter of the food items available in school canteens were classified as prohibited based on a new revised list of prohibited food and beverage items. These findings indicate that, despite the Guidelines, a large number of unhealthy food items are being sold in school canteens. Hence, interventions such as sustainable healthy school canteen menus should be implemented to promote healthy food choices amongst school-aged children.