Background Few studies have compared overweight and obesity in intellectually disabled (ID) and non‐intellectually disabled (N‐ID) children. This research compared the prevalence of overweight and obesity between a sample of 218 ID and 229 N‐ID school pupils in Northern Ireland (NI). Comparison of the physical activity and dietary behaviour of the two groups of school pupils were also undertaken. Methods Each pupil completed (assisted if required) a food intake and physical activity questionnaire. Following this body mass index (BMI) and waist circumference were measured and recorded. Results Significantly more ID pupils (72, 33%) were overweight/obese compared with 55 (24%) of the N‐ID pupils in accordance with their BMI. ID pupils also had significantly higher waist circumferences. Over a quarter of foods consumed by the pupils were fatty and sugary foods and close to 30% of these foods were eaten by the ID children. Pupils spent most of their time engaging in low levels of activity such as reading, watching TV, on games consoles and listening to music. Pupils with an ID spent fewer hours on moderate and high levels of activities compared with those children with N‐ID. Conclusions Results of this study found higher levels of overweight and obesity in this sample than in international published research. Additionally significantly higher numbers of ID pupils were overweight and obese indicating the need for future research and public health to focus on this issue.