Entrainment is known to alter or synchronize brain rhythm and may enhance task performance. However, whether and how sensory entrainment may modulate the long-range brain functional networks are unknown. We investigated the effects of frequency-dependent visual entrainment on resting state functional connectivity in distinct sensory cortical networks. Our findings provide the first and direct evidence that only low frequency visual entrainment can modulate the long-range non-visual sensory networks. They suggest that the entrained neural oscillation at low frequency can actively contribute to the long-range interactions between primary sensory cortical functional networks that underlie the brainwide connectivity measured by resting-state fMRI.