Stroke causes a sudden disruption of physiological brain function which leads to impairments of functional brain networks involved in voluntary movements. In some cases, the brain has the intrinsic capacity to reorganize itself, thereby compensating for the disruption of motor networks. In humans, such reorganization can be investigated in vivo using neuroimaging. Recent developments in connectivity analyses based on functional neuroimaging data have provided new insights into the network pathophysiology underlying neurological symptoms. Here we review recent neuroimaging studies using functional resting-state correlations, effective connectivity models or graph theoretical analyses to investigate changes in neural motor networks and recovery after stroke. The data demonstrate that network disturbances after stroke occur not only in the vicinity of the lesion but also between remote cortical areas in the affected and unaffected hemisphere. The reorganization of motor networks encompasses a restoration of interhemispheric functional coherence in the resting state, particularly between the primary motor cortices. Furthermore, reorganized neural networks feature strong excitatory interactions between fronto-parietal areas and primary motor cortex in the affected hemisphere, suggesting that greater top-down control over primary motor areas facilitates motor execution in the lesioned brain. In addition, there is evidence that motor recovery is accompanied by a more random network topology with reduced local information processing. In conclusion, Stroke induces changes in functional and effective connectivity within and across hemispheres which relate to motor impairments and recovery thereof. Connectivity analyses may hence provide new insights into the pathophysiology underlying neurological deficits and may be further used to develop novel, neurobiologically informed treatment strategies.