Background: The acute phase of stroke is accompanied by functional changes and interplay of both hemispheres. However, our understanding of how the time course of upper limb functional motor recovery is related to the progression of brain reorganization in the sensorimotor areas remains limited. This study aimed to assess the time course of hemodynamic patterns of cortical sensorimotor areas using functional near infrared spectroscopy (fNIRS) and motor recovery within three months after a stroke. Method: Eight right-handed first ischemic/hemorrhagic stroke patients (60±8 years, 3 women) with mild to severe hemiparesis were examined with repetitive fNIRS measurements and motor recovery tests (Fugl-Meyer score) during two months. Hemodynamic changes over the ipsilesional and contralesional sensorimotor areas were collected from a multi-channel fNIRS system during intermittent isometric muscle contractions at self-selected submaximal force levels for each arm. Lateralization index was computed to evaluate the changes in the interhemispheric balance between the cortical sensorimotor areas. Results: Lateralization index values during non-paretic arm movements showed no significant changes over time in patients and were comparable to those observed in eight healthy controls. Paretic-arm movements were associated early with a bilateral cortical activity before shifting to ipsilesional patterns (p < 0.01). Progressive lateralization observed over the two months (p < 0.05) evolved concomitantly with an increase in the Fugl-Meyer score (p < 0.001). Conclusions: Cortical reorganization monitoring using fNIRS during the first weeks after stroke may be applied for assessing progressive brain plasticity in addition to clinical measures of performance.