Recently, environmental problems caused by global warming and exhaust gas have been increasing, leading governments all over the world to implement strict environmental regulations. For this reason, the automotive industry has begun working to increase fuel efficiency and reduce emissions. In addition, in order to improve the performance of engines implemented in internal combustion engines (ICEs) and hybrid electric vehicles (HEVs), electronic control actuators are becoming increasingly preferred over conventional mechanical parts. In particular, engine intake and exhaust valve timing techniques are critical to improving fuel economy and reducing vehicle emissions. Previously, a hydraulic continuous variable valve timing (CVVT) system was used for valve timing control. However, a disadvantage of this type of system is that the response speed is slow at low and high engine temperatures; these conditions limit the extent of automobile fuel efficiency improvement. Therefore, an electric variable valve timing system (E-CVVT) is being studied to overcome this disadvantage. In this paper, we propose a shape optimum design method for brushless DC (BLDC) motors used in an electric continuous variable valve timing (E-CVVT) system, which is employed in ICEs and HEVs. The proposed design aims to maximize the maximum torque and rated efficiency of BLDC motors, and minimize cogging torque. To select the optimal design variables, we chose to implement Latin hypercube sampling (LHS) to avoid duplication of sampling points. The characteristics of the sampling points obtained via the LHS method were calculated by using finite element (FE) analysis. In order to consider the nonlinearity of properties, we have created an approximate modeling technique that uses a radial basis function. Finally, genetic algorithms were used to determine the design parameters of the optimum model. The effectiveness of the proposed BLDC motor design process is verified by comparing the FE analysis and experimental results. Simulation and experimental results confirmed that the proposed optimized design procedure yields improved operating characteristics. Specifically, testing the proposed optimized design yielded a 16.7% increase in the maximum torque, and a 66.2% reduction in the cogging torque. In addition, the vehicle test confirmed that the proposed design was suitable for an E-CVVT system equipped with a BLDC motor. In addition, the optimum model of the BLDC motor was applied to the E-CVVT system. The response characteristics of the conventional hydraulic CVVT system and E-CVVT were compared via vehicle testing. The response speed of the E-CVVT system was 0.65 s faster than that of the CVVT system during the retard angle phase. Therefore, it was a 39.4% improvement in the response performance.