Although motor imagery is widely used for motor learning in rehabilitation and sports training, the underlying mechanisms are still poorly understood. Based on fMRI data sets acquired with very high temporal resolution (300 ms) under motor execution and imagery conditions, we utilized Dynamic Causal Modeling (DCM) to determine effective connectivity measures between supplementary motor area (SMA) and primary motor cortex (M1). A set of 28 models was tested in a Bayesian framework and the by-far best-performing model revealed a strong suppressive influence of the motor imagery condition on the forward connection between SMA and M1. Our results clearly indicate that the lack of activation in M1 during motor imagery is caused by suppression from the SMA. These results highlight the importance of the SMA not only for the preparation and execution of intended movements, but also for suppressing movements that are represented in the motor system but not to be performed.