Tourette syndrome (TS) is a childhood-onset chronic disorder characterized by the presence of multiple motor and vocal tics. This study investigated the alterations of spontaneous brain activities in children with TS by resting-state functional magnetic resonance imaging (rs-fMRI). We obtained rs-fMRI scans from 21 drug-naive and pure TS children and 29 demographically matched healthy children. The amplitude of low-frequency fluctuation (ALFF), fractional ALFF (fALFF) and regional homogeneity (ReHo) of rs-fMRI data were calculated to measure spontaneous brain activity. We found significant alterations of ALFF or fALFF in vision-related structures including the calcarine sulcus, the cuneus, the fusiform gyrus, and the left insula in TS children. Decreased ReHo was found in the right cerebellum. Further analysis showed that the ReHo value of the right cerebellum was positively correlated with TS duration. Our study provides empirical evidence for abnormal spontaneous neuronal activity in TS patients, which may implicate the neurophysiological mechanism in TS children. Moreover, the right cerebellum can be potentially used as a biomarker for the pathophysiology of early TS in children.