There is growing interest in how the brain's motor systems contribute to the perception of musical rhythms. The Action Simulation for Auditory Prediction hypothesis proposes that the dorsal auditory stream is involved in bidirectional interchange between auditory perception and beat-based prediction in motor planning structures via parietal cortex [Patel, A. D., & Iversen, J. R. The evolutionary neuroscience of musical beat perception: The Action Simulation for Auditory Prediction (ASAP) hypothesis. Frontiers in Systems Neuroscience, 8, 57, 2014]. We used a TMS protocol, continuous theta burst stimulation (cTBS), that is known to down-regulate cortical activity for up to 60 min following stimulation to test for causal contributions to beat-based timing perception. cTBS target areas included the left posterior parietal cortex (lPPC), which is part of the dorsal auditory stream, and the left SMA (lSMA). We hypothesized that down-regulating lPPC would interfere with accurate beat-based perception by disrupting the dorsal auditory stream. We hypothesized that we would induce no interference to absolute timing ability. We predicted that down-regulating lSMA, which is not part of the dorsal auditory stream but has been implicated in internally timed movements, would also interfere with accurate beat-based timing perception. We show (n = 25) that cTBS down-regulation of lPPC does interfere with beat-based timing ability, but only the ability to detect shifts in beat phase, not changes in tempo. Down-regulation of lSMA, in contrast, did not interfere with beat-based timing. As expected, absolute interval timing ability was not impacted by the down-regulation of lPPC or lSMA. These results support that the dorsal auditory stream plays an essential role in accurate phase perception in beat-based timing. We find no evidence of an essential role of parietal cortex or SMA in interval timing.