Background Attention deficit hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) show significant behavioural and genetic overlap. Both ADHD and ASD are characterised by poor performance on a range of cognitive tasks. In particular, increased response time variability (RTV) is a promising indicator of risk for both ADHD and ASD. However, it is not clear whether different indices of RTV and changes to RTV according to task conditions are able to discriminate between the two disorders. Methods Children with ASD (n = 19), ADHD (n = 18), ASD + ADHD (n = 29) and typically developing controls (TDC; n = 26) performed a four‐choice RT task with slow‐baseline and fast‐incentive conditions. Performance was characterised by mean RT (MRT), standard deviation of RT (SD‐RT), coefficient of variation (CV) and ex‐Gaussian distribution measures of Mu, Sigma and Tau. Results In the slow‐baseline condition, categorical diagnoses and trait measures converged to indicate that children with ADHD‐only and ASD + ADHD demonstrated increased MRT, SD‐RT, CV and Tau compared to TDC and ASD‐only. Importantly, greater improvement in MRT, SD‐RT and Tau was demonstrated in ADHD and ASD + ADHD from slow‐baseline to fast‐incentive conditions compared to TDC and ASD‐only. Conclusions Slower and more variable RTs are markers of ADHD compared to ASD and typically developing controls during slow and less rewarding conditions. Energetic factors and rewards improve task performance to a greater extent in children with ADHD compared to children with ASD. These findings suggest that RTV can be distinguished in ASD, ADHD and ASD + ADHD based on the indices of variability used and the conditions in which they are elicited. Further work identifying neural processes underlying increased RTV is warranted, in order to elucidate disorder‐specific and disorder‐convergent aetiological pathways.