Disclosed is a method for predicting disease based on a medical image performed by a computing device. The method includes: generating a feature vector related to predictive values of brain disease for each of 2D medical images included in a 3D medical image, using a pre-trained first model; estimating importance indicating prediction accuracy for each of the 2D medical images based on the feature vector, using a pre-trained second model; and selecting at least one model input image suitable for prediction of the brain disease from among the 2D medical images based on the importance.