An apparatus for estimating a malignant tumor includes: a segmentor configured to segment a first medical image of an object into a first ROI including a mass and a second medical image of the object into a second ROI including a mass; an interest region determiner configured to acquire a first matched ROI and a second matched ROI, which is matched to the first matched ROI based on location information of the first ROI and the second ROI, respectively; a feature extractor configured to extract a similar feature indicating a degree of similarity between the first matched ROI and the second matched ROI, from the first matched ROI and the second matched ROI; and a classifier configured to generate malignant tumor information indicating whether the mass included in the first matched ROI and the second matched ROI is the malignant tumor, based on the extracted similar feature.