Surface deflection is a phenomenon that causes fine wrinkles on the outer surfaces of sheet metal and deteriorates product external appearance. It is quantitatively defined as the difference between the section curve of the sheet and the ideal curve. In this study, using neural networks, a prediction model for surface deflection according to material properties was constructed and combined with a genetic algorithm; the combination of the material properties was studied to predict the minimum surface deflection. Because of the limited number of simulation data, neural networks were developed using several sampling methods such as central composite design, Latin hypercube sampling, and random sampling. In the training of the neural networks, the optimal hyper-parameter of the neural network was found automatically using Latin hypercube sampling. In conclusion, for prediction of surface deflection in rectangular embossing, neural networks made by central composite design showed the best performance. In addition, it was confirmed that the procedure of combining automatic training of a neural network and the genetic algorithm accurately predicted the set of material properties that generates the minimum surface deflection. Also, the quantity of surface deflection predicted by the neural network was very close to that predicted by finite element analysis.