Background: We aim to assess the resting state functional connectivity (RSFC) and reactivity with functional near-infrared spectroscopy (fNIRS) in patients with acute stroke compared to age, sex and comorbidity-matched subjects. Methods: Patients with acute anterior circulation stroke syndrome localizing to the right (RH) or left hemisphere (LH) were enrolled. RSFC was assessed using group-level seed-based (Primary Motor cortex,PMC) correlation analysis. Finger-tapping-associated relative oxygen Hemoglobin (ΔHbO) changes were analyzed with generalized linear model regression. Results: 127 participants (RH stroke, 51; LH stroke, 43; control, 33) enrolled at a median of 21 (15,29) hours after symptom onset. Compared to the control group, the RSFC with the affected PMC (LH stroke) was reduced over the affected somatosensory cortex (SSC) in the minor ischemic stroke (IS) (r = -0.14 (-0.3,-0.01)), minor intracerebral hemorrhage (ICH) (-0.48 (-0.78,-0.18)) and major ICH groups (-0.2 (-0.4,-0.01). In the FT task compared to the control groups in LH stroke, ΔHbO was increased over the affected SSC in minor IS (β11.2(1.9,20.5)) and major ICH group (β11.7 (1.4,22.1)). In the FT task in RH stroke, ΔHbO was increased over the unaffected PMC in minor IS (β12.1(2.3,21.8)), major IS (β14.9 (0.3,29.5)), minor ICH (β25.7 (10.1,41.2)) and major ICH (β13.4 (1.1,25.6). Conclusions: Motor cortex dysconnectivity may be worse over the LH stroke. In RH stroke, there is early compensatory increased neuronal activity over the unaffected PMC. These results suggest differential acute remodelling in RH and LH strokes.