Internalising symptoms are elevated in autism compared to the general population. Few studies have investigated emotional dysregulation (ED) as a potential mediator between specific transdiagnostic processes and anxiety and depression symptoms in autistic youth. In a sample of 94 autistic young people aged 5-18 years referred to a specialist clinic for an autism evaluation, we tested the effects of ED as a mediator between cognitive inflexibility (CI), intolerance of uncertainty (IU) and alexithymia with anxiety and depression symptoms, using structural equation modelling. Effect sizes were compared to a non-autistic comparison group (n = 84). CI and alexithymia did not significantly predict depression symptoms in autistic young people, directly nor via ED. Relationships between CI/alexithymia and depression were fully mediated by ED in the non-autistic sample. There was a direct effect of CI on anxiety in the non-autistic group but not in those with a diagnosis. IU predicted depression symptoms in the autism group; and ED mediated this relationship only in those who did not receive a diagnosis. IU directly predicted anxiety in both groups and this relationship did not occur via ED. The finding of a direct pathway from IU to anxiety and depression in autistic youth is consistent with the literature. The finding that CI did not predict anxiety or depression in those with autism is novel, as was the finding that ED mediated relationships between alexithymia and anxiety/depression symptoms in both samples. The findings may have important implications for the delivery of psychological interventions for autistic youth.