Childhood dystonia is a disorder that involves inappropriate muscle activation during attempts at voluntary movement. Few studies have investigated the muscle activity associated with dystonia in children, and none have done so in the hands. In this study, we measured surface electromyographic activity in four intrinsic hand muscles while participants attempted to perform an isometric tracking task using one of the muscles. Children with dystonia had greater tracking error with the task-related muscle and greater overflow to non-task muscles. Both tracking error and overflow correlated with the Barry-Albright Dystonia scale of the respective upper limb. Overflow also decreased when participants received visual feedback of non-task muscle activity. We conclude that two of the motor deficits in childhood dystonia—motor overflow and difficulties in actively controlling muscles—can be seen in the surface electromyographic activity of individual muscles during an isometric task. As expected from results in adults, overflow is an important feature of childhood dystonia. However, overflow may be at least partially dependent on an individual’s level of awareness of their muscle activity. Most importantly, poor single-muscle tracking shows that children with dystonia have deficits of individual muscle control in addition to overflow or co-contraction. These results provide the first quantitative measures of the muscle activity associated with hand dystonia in children, and they suggest possible directions for control of dystonic symptoms.