Children with Developmental Coordination Disorder (DCD) present impaired motor skills, frequently associated with impaired attentional and executive functions. The objective of this study was to assess the impact of DCD on effective connectivity applied to a putative model of inhibition. fMRI was performed in 9 children with DCD and 10 control children (8-13 years old) performing a go-nogo task. As previously reported, children with DCD obtained a similar score for correct inhibitions as controls, but responses were slower and more variable than in controls. Compared to controls, Structural Equation Modeling indicated that: (1) path coefficients from both middle frontal cortex (MFC) and anterior cingulate cortex (ACC) to inferior parietal cortex (IPC) increased in children with DCD particularly in the left hemisphere; (2) path coefficients between striatum and parietal cortex decreased in children with DCD in the right hemisphere. Results suggest that DCD could be characterized by abnormal brain hemispheric specialization during development. Furthermore, connectivity in the MFC-ACC-IPC network could indicate that children with DCD are less able than healthy children to easily and/or promptly switch between go and nogo motor responses. However, children with DCD seem to compensate for this poor efficiency by more actively engaging the ACC to prevent commissions allowing maintenance of a good level of inhibition.