A randomized comparative prospective 35-day clinical-instrumental trial of 30 patients with ischemic hemispheric stroke hospitalized on the day of onset was performed. In the 16 patients of the study group, the antioxidant energy-correcting agent cytoflavin was added to basal treatment using the protocol: 20 ml/day by i.v. infusion on days 1–10; 2 tablets twice daily on days 11–35. The 14 reference patients received only basal treatment. Patients’ status was assessed at 0–24 h, and on post-stroke days 5, 11, 21, and 35. Neurological status was assessed using the Glasgow Scale, the NIH Stroke Scale, and the Mini Mental State Examination (MMSE); brain MRI scan scans were performed (to assess brain lesion volume); markers of antioxidant stress were assessed; functional disease outcomes were assessed using the Bartel index and a modified Rankin Scale. Early active correction of energy and free radical homeostasis with cytoflavin was found to lead to better improvements in morphological changes in the brain and free radical parameters, which correlated with the more significant and earlier (than in the control group) activation of consciousness and regression of neurological deficit; additional treatment also led to decreases in disability.