Background: The finding of positive outcomes at the group level for children with autism spectrum disorder (ASD) who complete comprehensive early intervention programmes often masks considerable individual variability. We therefore aimed to identify subgroups of children based on their response to intervention and to compare outcome variables between groups at two points in time. Method: We used model-based cluster analysis to explore response to intervention using a longitudinal design for 210 children with ASD who had completed an early intervention programme. Children were assessed on entry at time 1 and again at time 2, which was after 12 months or when they exited the programme (whichever came first) using measures of ASD symptoms (Social Communication Questionnaire), cognition (Mullen Scales of Early Learning) and adaptive behaviour (Vineland Adaptive Behaviour Scales-II). Results: A two-cluster solution was identified, including a high change group who improved consistently more than the low change group across measures, and showed significantly fewer autism symptoms, higher non-verbal and verbal cognition and adaptive behaviour composite scores at time 1. Conclusions: The findings indicated that children's response to early intervention is not uniform but instead included subgroups characterised by patterns of high and low change. Further research is needed to identify clinically relevant mediators of differential response group membership.