Continuous theta burst stimulation (cTBS) is a technique that allows for altering of brain activity. Research to date has focused on the effect of cTBS on the target area, but less is known about its effects on the resting state functional connectivity between different brain regions. We investigated this issue by applying cTBS to the occipital cortex and probing its influence in retinotopically defined regions in early visual cortex using functional MRI. We found that occipital cTBS reliably decreased the resting state functional connectivity (i.e., the correlation of spontaneous activity) between regions of the early visual cortex. In the context of a perceptual task, such an effect could mean that cTBS affects the strength of the perceptual signal, its variability, or both. We investigated this issue in a second experiment in which subjects performed a perceptual discrimination task and indicated their level of certainty on each trial. The results showed that occipital cTBS decreased both subjects' accuracy and confidence. Signal detection modeling suggested that these impairments resulted primarily from a decreased strength of the perceptual signal, with a nonsignificant trend of a decrease in signal variability. We discuss the implications of these experiments for understanding the mechanisms by which cTBS influences brain activity and perceptual processes.