Functional neuroimaging studies of handedness have traditionally focused on exploring regionally activated discrepancies, yet little is known regarding the effect of handedness on functional connections of brain regions. Here, we reported the relationship between cerebellar functional connectivity patterns and handedness by low-frequency blood oxygenation level-dependent fluctuations. Compared with the right-handers, the left-handers show higher cerebellar-prefrontal, cerebellar-parietal, and cerebellar-temporal functional connectivity, and lower cerebellar-limbic connectivity. Previous non-human primate studies have shown that these regions with known contributions to higher cognitive functions have afferent or efferent connections with the cerebellum. Our findings suggest that these observed low-frequency fluctuation correlations may reflect actually anatomic connections between the cerebellum and cerebral cortex, and the cerebellar involvement in higher function may be associated with handedness.