In the present study, the neural network (NN) model with cluster analysis method was developed to predict storm surge in the whole Korean coastal regions with special focuses on the regional extension. The model used in this study is NN model for each cluster (CL-NN) with the cluster analysis. In order to find the optimal clustering of the stations, agglomerative method among hierarchical clustering methods was used. Various stations were clustered each other according to the centroid-linkage criterion and the cluster analysis should stop when the distances between merged groups exceed any criterion. Finally the CL-NN can be constructed for predicting storm surge in the cluster regions. To validate model results, predicted sea level value from CL-NN model was compared with that of conventional harmonic analysis (HA) and of the NN model in each region. The forecast values from NN and CL-NN models show more accuracy with observed data than that of HA. Especially the statistics analysis such as RMSE and correlation coefficient shows little differences between CL-NN and NN model results. These results show that cluster analysis and CL-NN model can be applied in the regional storm surge prediction and developed forecast system.