Background: Dog-assisted therapy (DAT) is hypothesized to help children with autism spectrum disorder (ASD) and Down syndrome (DS). Methods: The present authors compared synchronous movement patterns of these children (n = 10) and their therapy dogs during the first and last session of a DAT programme, and their post-therapy changes in emotional and behavioural problems. Results: The present authors found a significant increase in synchrony between child and therapy dog over time. Exploratory analyses suggest more synchrony between children with ASD and their therapy dogs, compared to the children with DS. Conclusions: This study is the first to test the synchrony hypothesis, shedding light upon a mechanism that may underlie the effect of DAT and how this may be different for children with ASD and DS.