Government statistics show that children with special educational needs and disabilities do not achieve as well academically as their peers, which impacts on later employment and socioeconomic circumstances. Addressing these inequalities is a key policy area which currently lacks a satisfactory evidence base. To explore the issue, the present study used data from the Scottish Longitudinal Study which contains data from the 1991, 2001 and 2011 censuses along with other administrative data, from a representative sample of the Scottish population. Using this large and longitudinal sample, the present study examines educational engagement, expectations and attainment for children with self-reported disability, controlling for other early childhood factors. The results show that children with mental health problems were at higher risk of leaving school early, and that children with learning difficulties were less likely to gain advanced qualifications. Neither limiting long-term illness in early childhood nor disability in adolescence were significant predictors of engagement, however, they did predict measures of academic expectation and attainment. Results suggest there is a critical phase for attainment, with area deprivation in early childhood but not adolescence being important for later educational inequalities.