The ability of the mammalian brain to modify existing memories through reconsolidation may be crucial for skill acquisition. The neural mechanisms of memory modification have been commonly studied at the cellular level. Yet surprisingly, the human brain systems-level mechanisms involved in day-to-day modification of existing procedural memories remain largely unknown. Here, we studied differences in fMRI regional signal activity and inter-regional functional connectivity in subjects in whom motor memory modification was interfered with by repetitive transcranial magnetic stimulation (rTMS), relative to subjects with intact memory modification. As a consequence, subjects with impaired memory modification had lower activity in the supplementary motor area (SMA) and weaker functional connectivity between M1, SMA, anterior cerebellum consistently engaged in early learning, and sensorimotor striatum active in later learning stages. These findings, identifying a link between engagement of this network and successful memory modification, suggest that memory reconsolidation may represent a transitional bridge between early and late procedural learning, underlying efficient skill acquisition.