The transition from primary to secondary school represents one of the key junctions in the educational career of young people. Research has shown that much of the challenge in this transition stems from changing social structures and encountering different learning environments. However, the transition experiences of students with special educational needs (SEN) have received relatively little attention. Drawing on large-scale longitudinal data from over 7000 young people, we examine the extent to which students with different SEN experience additional transition barriers to their peers. The findings show that young people with SEN are more likely to experience a negative transition to secondary school. Furthermore, the type of need matters and students with general learning disabilities and intellectual disabilities are three times more likely to experience poor transition compared to young people without SEN. Transition experiences also vary by gender and socio-economic status, with girls and lower socio-economic groups more at risk. This paper highlights the importance of supporting students through to their second year in secondary education, promoting positive teacher-student interactions and providing additional supports for those with lower achievement in primary school. For students with disabilities, the research highlights a need for more effective transition supports, particularly during the pre-transition period.