Functional connectivity differences between children with autism spectrum disorder (ASD) and typically developing children have been described in multiple datasets. However, few studies examine the task‐related changes in connectivity in disorder‐relevant behavioral paradigms. In this paper, we examined the task‐related changes in functional connectivity using EEG and a movement‐based paradigm that has behavioral relevance to ASD. Resting‐state studies motivated our hypothesis that children with ASD would show a decreased magnitude of functional connectivity during the performance of a motor‐control task. Contrary to our initial hypothesis, however, we observed that task‐related modulation of functional connectivity in children with ASD was in the direction opposite to that of TDs. The task‐related connectivity changes were correlated with clinical symptom scores. Our results suggest that children with ASD may have differences in cortical segregation/integration during the performance of a task, and that part of the differences in connectivity modulation may serve as a compensatory mechanism. Autism Res 2017. © 2017 International Society for Autism Research, Wiley Periodicals, Inc. Lay Summary Decreased connectivity between brain regions is thought to cause the symptoms of autism. Because most of our knowledge comes from data in which children are at rest, we do not know how connectivity changes directly lead to autistic behaviors, such as impaired gestures. When typically developing children produced complex movements, connectivity decreased between brain regions. In children with autism, connectivity increased. It may be that behavior‐related changes in brain connectivity are more important than absolute differences in connectivity in autism.