Friedreich's ataxia (FRDA) is the most common form of hereditary ataxia. In addition to proximal spinal cord and brain stem atrophy, mild to moderate atrophy of the cerebellum has been reported in advanced FRDA. The aim of this study was to examine dysfunction in motor-related areas involved in the execution of finger tapping tasks in individuals with FRDA, and to investigate functional re-organization of cortico-cerebellar, cortico-striatal and parieto-frontal loops as a result of the cerebellar pathology. Thirteen right-handed individuals with FRDA and fourteen right-handed controls participated. Functional MRI images were acquired during four different finger tapping tasks consisting of visually cued regular and irregular single finger tapping tasks, a self-paced regular finger tapping task, and a visually cued multi-finger tapping task. Both groups showed significant activation of the motor-related network including the pre-central cortex and supplementary motor area bilaterally; the left primary motor cortex, somatosensory cortex and putamen; and the right cerebellum. During the visually cued regular finger tapping task, the right hemisphere of the cerebellar cortex, bilateral supplementary motor areas and right inferior parietal cortex showed higher activation in the healthy control group, while in individuals with FRDA the left premotor cortex, left somatosensory cortex and left inferior parietal cortex were more active. In addition, during the visually cued irregular finger tapping task, the right middle temporal gyrus in the control group and the right superior parietal lobule and left superior and middle temporal gyri in the individuals with FRDA showed higher activation. During visually cued multi-finger tapping task, the control group showed higher activation in the bilateral middle frontal gyri, bilateral somatosensory cortices, bilateral inferior parietal lobules, left premotor cortex, left supplementary area, right superior frontal gyrus and right cerebellum, while individuals with FRDA showed increased activity in the left inferior parietal lobule, left primary motor cortex, left middle occipital gyrus, right somatosensory cortex and the left cerebellum. Only the right crus I/II of the cerebellum showed higher activation in individuals with FRDA during the self-paced regular finger tapping task, whereas wide-spread regions including the left superior frontal gyrus, left central opercular cortex, left somatosensory cortex, left putamen, right cerebellum, bilateral primary motor cortices, bilateral inferior parietal lobules and the left insula were more active in the control group. Although the pattern of the BOLD signal from the putamen was different during the self-paced regular finger tapping task to the other tasks in controls, in individuals with FRDA there was no distinction of the signal between the tasks suggesting that primary cerebellar pathology may cause secondary basal ganglia dysregulation. While individuals with FRDA tapped at a slightly lower rate (0.59Hz) compared with controls (0.74Hz) they showed significantly decreased activity of the SMA and the inferior parietal lobule, which may suggest disruption to the fronto-parietal connections. These findings suggest that the motor impairments in individuals with FRDA result from dysfunction extending beyond the spinal cord and cerebellum to include sub-cortical and cortical brain regions.