In the past few decades, several countries have introduced reforms aimed at increasing school autonomy. We evaluate the effect of the introduction of autonomous academies in England on the educational trajectories of children with special educational needs. This has been done using longitudinal data on all schoolchildren in state schools in England, from the National Pupil Database. The results show that the effects of school autonomy on educational inclusion are not uniform and depend on schools' previous performance and socio-economic composition. Schools that obtained autonomy under the control of an external sponsor (sponsored academies) were more likely to decrease the proportion of pupils with special needs and remove additional support for them. We do not observe these effects in the schools that voluntarily applied for the more autonomous status (converter academies).