The neural correlates of motor imagery (MI) are tightly coupled with the cortical motor control network. Therefore MI may have therapeutic potential for patients with motor deficits after an ischemic stroke. The aim of our study was to assess the hemispheric balance of the cortical motor network during motor imagery (MI) in patients recovering from stroke in the sub-acute stage. We studied 17 patients after cerebral ischemic stroke (sub-acute stage) and 12 healthy subjects using functional Magnetic Resonance Imaging (fMRI) during motor imagery and performance of isometric grip force movements (5 Newton). Laterality indices (LI) were calculated from regional activation analysis to assess hemispheric distribution of activity in pre-specified motor areas. Laterality index (LI) revealed a more balanced cortical activity in MI for both controls (-0.03) and patients (-0.12) in the premotor cortex compared to movement execution (0.48 controls; 0.12 patients) and a trend towards a shift in contra-lesional activity in stroke patients. Our results indicate a preserved interhemispheric balance of patients in the sub-acute stage when activating the cortical motor areas during MI. This could provide a reasonable physiologic baseline for using MI as an additional rehabilitative therapy for improving functional recovery in the sub-acute stage after stroke.