The ability to control external events through our own actions is a fundamental aspect of human experience. Both the subjective experience of agency, and its neural correlates, remain poorly understood. Previous studies show that the angular gyrus is activated when participants explicitly judge that they lack agency. In contrast, the positive sense of agency over external events is associated with distortions of time perception. Here, we show that the perceived interval between actions and a subsequent tone is shorter than the perceived interval between a physically comparable passive movement and a tone, replicating the ‘intentional binding’ effect reported previously. We considered this as a potential implicit marker of agency, and investigated its neural basis, by using parametric analyses to identify brain areas whose activation correlated more strongly with the perceived action-tone interval in the action condition, than in the passive condition. Small volume corrections were used to test specific hypotheses about the contribution of the angular gyrus, and of the supplementary motor area (SMA), based on previous literature. We found no correlation between angular gyrus and our temporal measure of sense of agency. In contrast, we found that a lateral, caudal region within the SMA proper was more strongly associated with the perceived action-tone interval than with perception of a control interval following a passive movement. We suggest that the supplementary motor complex contributes to the subjective experience of temporal flow that accompanies goal-directed voluntary actions.