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High-definition transcranial direct current stimulation (HD-tDCS) has recently been proposed as a tDCS approach that can be used on a specific cortical region without causing undesirable stimulation effects. In this uncontrolled pilot study, the cortical hemodynamic changes caused by HD-tDCS applied over the ipsilesional motor cortical area were investigated in 26 stroke patients. HD-tDCS using one anodal and four cathodal electrodes at 1 mA was administered for 20 min to C3 or C4 in four daily sessions. Cortical activation was measured as changes in oxyhemoglobin (oxyHb) concentration, as found using a functional near-infrared spectroscopy (fNIRS) system during the finger tapping task (FTT) with the affected hand before and after HD-tDCS. Motor-evoked potential and upper extremity functions were also measured before (T0) and after the intervention (T1). A group statistical parametric mapping analysis showed that the oxyHb concentration increased during the FTT in both the affected and unaffected hemispheres before HD-tDCS. After HD-tDCS, the oxyHb concentration increased only in the affected hemisphere. In a time series analysis, the mean and integral oxyHb concentration during the FTT showed a noticeable decrease in the channel closest to the hand motor hotspot (hMHS) in the affected hemisphere after HD-tDCS compared with before HD-tDCS, in accordance with an improvement in the function of the affected upper extremity. These results suggest that HD-tDCS might be helpful to rebalance interhemispheric cortical activity and to reduce the hemodynamic burden on the affected hemisphere during hand motor tasks. Noticeable changes in the area adjacent to the affected hMHS may imply that personalized HD-tDCS electrode placement is needed to match each patient’s individual hMHS location.