Sense of agency (SoA) refers to the experience of controlling one’s own actions. Temporal distortions between the action and the effect mislead agency attribution. We investigated the covariance between the amount of functional interactions among brain regions at rest and SoA. We found that the functional network involved in self-agency attribution included the premotor and somatosensory cortices bilaterally, and the right superior parietal lobule. This provides the first evidence that functional connectivity at rest in healthy subjects varies along with experienced SoA, implying that self-agency is processed within an intrinsic brain functional module.