In Tourette syndrome (TS), not only the tics but also the findings on deficits in motor performance indicate motor system alterations. But our knowledge about the pathophysiology of the motor system in TS is still limited. To better understand the neuronal correlates of motor performance in TS, 19 treatment-naïve boys [age 12.5 (SD 1.4) years] with TS without comorbid symptomatology were compared to an age-matched healthy control group [n = 16; age 12.9 (SD 1.6) years] in regard to brain activation during right-hand index finger tapping by means of functional magnetic resonance imaging. Group differences were found mainly in the left (contralateral) precentral gyrus, which was less activated in boys suffering from TS and in caudate nucleus as well as in medial prefrontal cortex, which was more activated compared to healthy boys. These results show that even in the first years after the onset of the disorder, an altered brain network of motor performance is recruited. These alterations in brain regions frequently associated with TS are probably based on functional changes, which are discussed in terms of early compensatory mechanisms of the motor execution network.