Pupils in alternative education provision, known as ‘Educated in Other Than At School’ (EOTAS) in Wales, UK, are among the most vulnerable learners and who, for reasons such as mental health or behavioural challenges, do not attend a mainstream or special school.

We compared self-harm, neurodevelopmental disorders and mental health conditions between EOTAS pupils and controls with similar characteristics, before and after being in EOTAS provision.

This population-based electronic cohort study included pupils in Wales aged 7–18 years, from the academic years 2010–11 to 2018–19. We linked data from Education Wales to primary and secondary healthcare records within the Secure Anonymised Information Linkage (SAIL) Databank. Individuals included in the EOTAS data-set were identified as cases. Controls were pseudo-randomly selected based on equivalent age and academic year distribution.

This study included 8056 pupils in EOTAS and 224 247 controls. Higher levels of deprivation, childhood maltreatment, self-harm, neurodevelopmental disorders and mental health conditions before EOTAS entry were linked to higher odds of being in EOTAS. Pupils in EOTAS provision had increased incidence of self-harm, neurodevelopmental disorders and mental health conditions, from 1 year after entering EOTAS provision up to 24 years of age, than pupils with similar characteristics not in EOTAS provision.

While EOTAS provision plays an important role, our findings indicate that it is not sufficient on its own to meet pupils’ social, emotional, behavioural and mental health needs. Additional support and better integration with health and social services are required.