Impaired sustained attention is considered an important factor in determining poor functional outcomes across multiple cognitive and behavioural disorders. Sustained attention is compromised for both children with Williams syndrome (WS) and Down's syndrome (DS), but specific difficulties remain poorly understood because of limitations in how sustained attention has been assessed thus far. In the current study, we compared the performance of typically developing children (N = 99), children with WS (N = 25), and children with DS (N = 18), on a Continuous Performance Task - a standard tool for measuring sustained attention. In contrast to previous studies, primarily focused on overall differences in mean performance, we estimated the extent to which performance changed over time on task, thus focusing directly on the sustained element of performance. Children with WS and children with DS performed more poorly overall compared to typically developing children. Importantly, measures specific to changes over time differentiated between children with the two syndromes. Children with WS showed a decrement in performance, whereas children with Down's syndrome demonstrated non-specific poor performance. In addition, our measure of change in performance predicted teacher-rated attention deficits symptoms across the full sample. An approach that captures dynamic changes in performance over assessments may be fruitful for investigating similarities and differences in sustained attention for other atypically developing populations.