The availability of a pre-existing cognitive-motor schema accelerates the learning of novel motor information. The encoding of a novel schema-compatible, compared with -incompatible, motor sequence was recently shown to be supported by the left primary motor cortex (M1). However, causal evidence for the role of M1 in schema-mediated motor learning is currently lacking. In the current study, we aimed to address this knowledge gap by transiently disrupting M1 using inhibitory continuous theta-burst stimulation (cTBS). Forty-eight young healthy participants learned a bimanual motor sequence task (cognitive-motor schema). Twenty-four hours later, they learned a novel sequence whose ordinal schematic structure was compatible with that learned on the previous day. To provide causal evidence for a role of M1 on such schema-mediated motor learning, we applied either cTBS or sham stimulation to the left M1 immediately before encoding the schema-compatible novel sequence. Electromyography results showed no evidence for an effect of left M1 cTBS on corticospinal excitability as measured with motor-evoked potentials. Similarly, behavioral results indicated no significant effect of cTBS on subsequent schema-mediated motor sequence learning. Altogether, the present data do not provide evidence for a causal role of the left M1 in schema-mediated motor sequence learning.NEW & NOTEWORTHY Primary motor cortex (M1) continuous theta-burst stimulation (cTBS) did not impair schema-mediated motor sequence learning compared with sham. M1 cTBS did not suppress corticospinal excitability at the group level. Across individuals, greater motor-evoked potential (MEP) suppression was related to higher baseline MEPs. Postintervention changes in MEP amplitude did not correlate with motor performance.