Purpose <p>Cognitive flexibility is a key neurocognitive process that is often challenging in children with autism. Recent research has highlighted the potential influence of motivation on cognitive flexibility; however, the impact of different types of motivation (intrinsic vs. extrinsic) on the cognitive flexibility performance of children with autism remains unclear.</p> Method <p>This study aims to investigate the impact of intrinsic and extrinsic motivation on cognitive flexibility in 43 children with autism and 89 typically developing children (TDC) (age range 36–84 months), using the three versions of dimensional change card sorting task (standard, extrinsic reward and intrinsic motivation versions).</p> Results <p>Results indicate that manipulating cognitive flexibility through motivation can improve performance, particularly in children with autism, with a significant impact of intrinsic motivation on this group. In the age range of 36–48 months, intrinsic motivation enhance accuracy in children with autism but not in TDC. From 49 to 60 months of age, both intrinsic and extrinsic motivation contribute to improved accuracy in children with Autism, with intrinsic motivation having a more significant impact. In TDC, however, only intrinsic motivation is associated with enhanced accuracy. In older children, both intrinsic and extrinsic motivation enhance performance in both groups, suggesting the maturation of cognitive systems. This evidence suggests that, in children with autism, the impact of motivation emerges at an earlier age than in typically developing children. Notably, intrinsic motivation has a more significant and profound effect at a younger age compared to extrinsic rewards.</p> Conclusion <p>The study provides insights into the developmental trajectory of cognitive flexibility in children with autism and highlights the significance of leveraging motivation to enhance this essential cognitive function.</p>