Traumatic brain injury (TBI) is a common form of disability in children. Persistent deficits in motor control have been documented following TBI but there has been less emphasis on changes in functional cerebral activity. In the present study, children with moderate to severe TBI (n 9) and controls (n 17) were scanned while performing cyclical movements with their dominant and non-dominant hand and foot according to the easy isodirectional (same direction) and more difficult non-isodirectional (opposite direction) mode. Even though the children with TBI were shown to be less successful on various items of a clinical motor test battery than the control group, performance on the coordination task during scanning was similar between groups, allowing a meaningful interpretation of their brain activation differences. fMRI analysis revealed that the TBI children showed enhanced activity in medial and anterior parietal areas as well as posterior cerebellum as compared with the control group. Brain activation generally increased during the non-isodirectional as compared with the isodirectional mode and additional regions were involved, consistent with their differential degree of difficulty. However, this effect did not interact with group. Overall, the findings indicate that motor impairment in TBI children is associated with changes in functional cerebral activity, i.e. they exhibit compensatory activation reflecting increased recruitment of neural resources for attentional deployment and somatosensory processing.