In humans the consolidation of recently learned motor skills is a multi-step process. We previously showed that performance on the finger-tapping task (FTT; i.e. a sequential motor skill) temporarily improves early on, 5–30 min after practice has ended, but not 4 h later. In the absence of any further practice to the task, this early boost in performance was predictive of the performance levels eventually achieved 48 h later, suggesting its functional relevance for long-term memory consolidation [Hotermans, Peigneux, Maertens de Noordhout, Moonen, and Maquet (2006) Early boost and slow consolidation in motor skill learning. Learn. Mem., 13, 580–583]. Here, we focused on the role of the primary motor cortex (M1) in consolidation using repetitive transcranial magnetic stimulation (rTMS) applied immediately before testing at 30 min, 4 or 24 h after practice of the FTT. Immediately after learning, rTMS over M1 depressed the early boost in performance, but did not affect the delayed improvement observed 48 h later. Four and 24 h after practice, rTMS did not disrupt performance anymore. These results suggest that M1 supports performance during the early post-training phase of motor skill consolidation, but is no longer mandatory in the subsequent, delayed stages of consolidation.