Recently, a large amount of research on deep learning has been conducted. Related studies have also begun to apply deep learning techniques to the field of electric machines, but such studies have been limited to the field of fault diagnosis. In this study, the shape optimization of a permanent magnet synchronous motor (PMSM) for electric vehicles (EVs) was conducted using a multi-layer perceptron (MLP), which is a type of deep learning model. The target specifications were determined by referring to Renault’s Twizy, which is a small EV. The average torque and total harmonic distortion of the back electromotive force were used for the multi-objective functions, and the efficiency and torque ripple were chosen as constraints. To satisfy the multi-objective functions and constraints, the angle between the V-shaped permanent magnets and the rib thickness of the rotor were selected as design variables. To improve the accuracy of the design, the design of experiments was conducted using finite element analysis, and a parametric study was conducted through analysis of means. To verify the effectiveness of the MLP, metamodels was generated using both the MLP and a conventional Kriging model, and the optimal design was determined using the hybrid metaheuristic algorithm. To verify the structural stability of the optimized model, mechanical stress analysis was conducted. Moreover, because this is an optimal design problem with multi-objective functions, the changes in the optimal design results were examined as a function of the changes in the weighting. The optimal design results showed that the MLP technique achieved better predictive performance than the conventional Kriging model and is useful for the shape optimization of PMSMs.