Student engagement is recognised as being necessary for students to achieve well academically. Much student engagement research is centred on the perceptions of students via self‐assessment or teacher questionnaires. For young students, particularly those with intellectual disability (ID), self‐assessment can be problematic due to their disability. Teacher questionnaires can also be difficult to administer in such students, as often the engagement behaviours or processes to be identified are internal. This study introduces a new student engagement checklist (SEC) developed to rate the observable task, affective and cognitive engagement behaviours of students with ID when working on academic tasks. The SEC was applied to video footage of five junior primary students with ID participating in 20 individual reading lessons. The study used an alternating‐treatments, single‐case design that enabled comparison of levels of engagement in two different lesson formats. This study indicates that the SEC can be used reliably to generate estimates of the task, affective and cognitive engagement components with the students involved. Importantly, the SEC provided relevant information on distinct elements of cognitive engagement, particularly highlighting the low levels of elaboration and monitoring behaviour, elements of cognitive engagement. This information has not been readily available in previous research. This study suggests that the SEC would be useful in further research on engagement with different types of students, not only those with limited language and cognitive delay.