Our sense of agency, the subjective experience of controlling our actions, is a crucial component of self-awareness and motor control. It is thought to originate from the comparison between intentions and actions across broad cortical networks. However, the underlying neural mechanisms are still not fully understood. We hypothesized that oscillations in the theta-alpha range, thought to orchestrate long-range neural connectivity, may mediate sensorimotor comparisons. To test this, we manipulated the relation between intentions and actions in a tetraplegic user of a brain machine interface (BMI), decoding primary motor cortex (M1) activity to restore hand functionality. We found that the pre-movement phase of low-alpha oscillations in M1 predicted the participant’s agency judgements. Further, using EEG-BMI in healthy participants, we found that pre-movement alpha oscillations in M1 and supplementary motor area (SMA) correlated with agency ratings, and with changes in their functional connectivity with parietal, temporal and prefrontal areas. These findings argue for phase-driven gating as a key mechanism for sensorimotor integration and sense of agency.