Background: Young people with intellectual disability exhibit substantial and persistent problem behaviours compared with their non-disabled peers. The aim of this study was to compare changes in emotional and behavioural problems for young people with intellectual disability with and without Down syndrome as they transition into adulthood in two different Australian cohorts. Methods: Emotional and behavioural problems were measured over three time points using the Developmental Behaviour Checklist (DBC) for those with Down syndrome (n = 323 at wave one) and compared to those with intellectual disability of another cause (n = 466 at wave one). Outcome scores were modelled using random effects regression as linear functions of age, Down syndrome status, ability to speak and gender. Results: DBC scores of those with Down syndrome were lower than those of people without Down syndrome indicating fewer behavioural problems on all scales except communication disturbance. For both groups disruptive, communication disturbance, anxiety and self-absorbed DBC subscales all declined on average over time. There were two important differences between changes in behaviours for these two cohorts. Depressive symptoms did not significantly decline for those with Down syndrome compared to those without Down syndrome. The trajectory of the social relating behaviours subscale differed between these two cohorts, where those with Down syndrome remained relatively steady and, for those with intellectual disability from another cause, the behaviours increased over time. Conclusions: These results have implications for needed supports and opportunities for engagement in society to buffer against these emotional and behavioural challenges.