The current paper examined the impact of the transition from primary to secondary school on anxiety for children with Neurodevelopmental Disorders (NDDs), specifically for autistic children, children with Down Syndrome (DS) and Williams Syndrome (WS). Previous research has highlighted the impact such educational changes can have upon autistic children, but there is only limited research for children with DS and none for those with WS. Hence, this study aimed to better understand whether school transitions have a unique or similar impact on anxiety through a cross-syndrome comparison. Sixty-one parents as well as their autistic children, children with DS and WS completed an online survey at two time-points, which included questions on adjustment and psychopathology, maladaptive behaviours, and other open-ended measures about their child’s skills as well as their experiences of the transition from primary to secondary school. Children themselves completed a short interview as well as a set of cognitive abilities tasks. Both children and parents of all three groups expressed concerns about bullying and adjustment to new environments during transition from primary to secondary school. Although wide variability was found within the autism, DS and WS groups, no significant differences were revealed in overall levels of parent-reported anxiety before and after the transition for any of the groups. However, different factors, including maladaptive behaviour, social problems and peer problems predicted anxiety during pre- and post-school transition for the three groups. This first cross-syndrome comparison on the effect of transition from primary to secondary school on anxiety highlighted the importance of individual variability when examining the transition outcomes of children with NDDs. Additionally, it identified clusters of overlap in terms of parent-report and child-report experiences of transition and unique predictors that need to be considered when planning transition support for autistic children, children with DS and WS. Future research should investigate the role of protective factors both at an individual and school level to inform the development of evidence-based intervention that support successful transition to secondary education.