As the demand for agricultural electric vehicles increases, it is becoming important to conduct noise reduction in consideration of the characteristics of an electric powertrain. This study was conducted to optimize the shape design of gearbox housing for radiated noise reduction of an agricultural electric vehicle gearbox. The noise and vibration of the gearbox were measured considering the noise characteristics of the electric vehicle gearbox, which radiates high-frequency pure tone noise. The main noise source radiated by the structural vibration of the gearbox housing was identified and considered when modeling the loading conditions in the numerical analysis. To improve the reliability, the finite element (FE) model was updated and validated. Internal machine elements were modeled as a substructure through a reduced-order modeling method to reduce the computing time and apply a constant gear excitation force. The weak areas of structure were determined and it was used as the design area for optimization. The topology optimization technique was used to reduce the equivalent radiated power (ERP) which was used as an indicator of radiated noise level. The maximum value of the ERP decreased under all operating conditions at the rated speed.