Dual-mode non-invasive brain stimulation using repetitive transcranial magnetic stimulation and transcranial direct current stimulation is known to help neurorehabilitation in patients with stroke. However, this neuromodulation effect may vary depending on the lesion location of patients with stroke, and the basis in lesion location for this is insufficient. This study aims to investigate the difference in neuromodulation effectiveness according to the lesion location after dual-mode brain stimulation using electroencephalography signals. Eight patients with ischemic subacute stroke and 11 healthy controls participated in this study. Brain stimulation was conducted in one session per day for a total of 10 days over the motor cortex, electroencephalography was measured for 5 min with eyes closed, and motor function was evaluated before and after dual-mode stimulation. The lesion location was divided into an infratentorial stroke (ITS) and a supratentorial stroke (STS) based on tentorium cerebelli. In addition, we focused on the mu and beta bands related to motor function. In terms of intrahemispheric connectivity, the mu weighted phase lag index over the contralesional primary motor cortex was significantly higher in only ITS before stimulation compared to healthy controls, and mu Granger causality over the ipsilesional primary motor cortex was significantly higher in both ITS and STS after stimulation compared to healthy controls. In contrast, from the perspective of interhemispheric connectivity, the laterality of beta Granger causality before stimulation in ITS was lower than that of healthy controls and significantly increased after stimulation. The effect of brain stimulation may vary depending on the lesion location of patients with stroke, and these findings provide indicative insights into effective dual-mode stimulation interventions for neurorehabilitation.