Theta burst transcranial magnetic stimulation (TBS) is considered to produce plastic changes in human motor cortex. Here, we examined the inhibitory and excitatory effects of TBS on implicit sequence learning using a probabilistic serial reaction time paradigm. We investigated the involvement of several cortical regions associated with implicit sequence learning by examining probabilistic sequence learning in five age- and IQ-matched groups of healthy participants following continuous inhibitory TBS over primary motor cortex (M1); or the supplementary motor area (SMA) or dorsolateral prefrontal cortex (DLPFC) or following intermittent excitatory TBS of M1; or after sham TBS. Relative to sham TBS, probabilistic sequence learning was abolished by inhibitory TBS over M1, demonstrating that this region is critical for implicit motor sequence learning. Sequence learning was not significantly affected by inhibitory TBS over the SMA, DLPFC or excitatory TBS over M1. These results demonstrate that the M1 mediates implicit sequence learning.