The notion that already existing memories can be modified after their reactivation has received an increasing amount of experimental support, with empirical data accumulating across species and memory paradigms. However, there is no evidence for systems-level task-free intrinsic signatures of memory modification. Here, using a combination of behavioral, brain stimulation, and neuroimaging paradigms, we report that noninvasive transcranial magnetic stimulation interference with a reactivated motor memory altered offline task-free corticostriatal interregional functional connectivity, reducing it compared to stimulation in which the reactivated memory was intact. Furthermore, the modulated functional connectivity predicted offline memory modification. This reduction in functional connectivity recovered after additional execution of the memorized task, and the interference did not affect control cerebellar-cortical functional connectivity. This demonstrates that intrinsic task-free offline brain activity can be modulated by noninvasive interaction with existing memories and strongly correlates with behavioral measurements of changes in memory strength.