Transition from primary to secondary school is an educational milestone that coincides with other key developmental changes associated with the onset of adolescence. Although previous studies have examined the impact of school transition on autistic students, no studies thus far have examined whether the impacts experienced are similar across different neurodivergent populations. In this paper, we examined how the transition to secondary school affects anxiety experienced by autistic children, children with Down syndrome (DS) and Williams syndrome (WS). Sixty-one parents completed an online survey at two time-points, answering questions about their neurodivergent child's anxiety, adjustment, well-being, skills, and experiences of the transition to secondary school. The children themselves completed a short interview, which included completing a set of standardised measures with a researcher. Both neurodivergent children and parents expressed concerns about bullying and adjustment to new environments during transition from primary to secondary school. Although wide variability was found in our sample, no significant differences were revealed in the overall levels of parent-reported anxiety pre- and post-transition. However, different factors predicted anxiety during pre- and post-school transition. The impact of these findings for theory and practice are discussed.