COVID-19 is considered one of the largest pandemics in recent times. Predicting the number of future COVID-19 cases is extremely important for governments in order to make decisions about mobility restrictions, and for hospitals to be able to manage medical supplies, as well as health staff. Most of the predictions of COVID-19 cases are based on mathematical-epidemiological models such as the SEIR and SIR models. In our work, we propose a model of neural networks GCN-LSTM (Graph Convolutional Network - Long Short Term Memory) to predict the spatio-temporal rate incidence of COVID-19 in the Metropolitana Region, Chile. While the GCN network incorporates the spatial correlation in the nearby municipalities, the LSTM network considers the temporal correlation for the prediction over time. To interpolate the missing daily data for the network input, the use of the GAM (Generalized Additive Model) model is proposed. The results show better predictions for some municipalities with higher habitat density.