Acute cerebral ischemia is commonly accompanied by cerebral edema. With brain electrical impedance tomography (EIT), it is possible to monitor conductivity variation during dehydration treatment of the cerebral edema. However, the scalp is also dehydrated when dehydrating brain tissue which exerts a large impact on boundary measurement. Consequently, reconstruction quality of cerebral edema is seriously affected. To reduce the influence of scalp dehydration, a voltage data compensation method based on a fully connected neural network (FCNN) is proposed in this work. With this method, the voltage measured when brain tissue and scalp are simultaneously dehydrated can be compensated. To evaluate the performance of the proposed method, reconstruction of simulated cerebral ischemia in a three-layer head model is conducted. Images reconstructed with the compensated voltage data are compared with the results when there is no compensation. Besides, quantitative comparison is performed. The results indicate that it is almost impossible to identify the simulated cerebral ischemia without voltage compensation. In contrast, cerebral ischemia can be much more accurately reconstructed when the measured voltage is compensated with the proposed method.