Functional neuroimaging studies frequently demonstrated that stroke patients show bilateral activity in motor and premotor areas during movements of the paretic hand in contrast to a more lateralized activation observed in healthy subjects. Moreover, a few studies modeling functional or effective connectivity reported performance-related changes in the motor network after stroke. Here, we investigated the temporal evolution of intra- and interhemispheric (dys-) connectivity during motor recovery from the acute to the early chronic phase post-stroke. Twelve patients performed hand movements in an fMRI task in the acute (≤72 hours) and subacute stage (2 weeks) post-stroke. A subgroup of 10 patients participated in a third assessment in the early chronic stage (3-6 months). Twelve healthy subjects served as reference for brain connectivity. Changes in effective connectivity within a bilateral network comprising M1, premotor cortex (PMC), and supplementary motor area (SMA) were estimated by dynamic causal modeling. Motor performance was assessed by the Action Research Arm Test and maximum grip force. Results showed reduced positive coupling of ipsilesional SMA and PMC with ipsilesional M1 in the acute stage. Coupling parameters among these areas increased with recovery and predicted a better outcome. Likewise, negative influences from ipsilesional areas to contralesional M1 were attenuated in the acute stage. In the subacute stage, contralesional M1 exerted a positive influence on ipsilesional M1. Negative influences from ipsilesional areas on contralesional M1 subsequently normalized, but patients with poorer outcome in the chronic stage now showed enhanced negative coupling from contralesional upon ipsilesional M1. These findings show that the reinstatement of effective connectivity in the ipsilesional hemisphere is an important feature of motor recovery after stroke. The shift of an early, supportive role of contralesional M1 into enhanced inhibitory coupling might indicate maladaptive processes which could be a target of non-invasive brain stimulation techniques.