The present work proposes a Multi-Output Classification Autoencoder (MOC-AE) algorithm to extract features from brain tumour images. The proposed algorithm is able to focus on both the normal features of the patient and the pathological features present in the case, resulting in a compact and significant representation of each image. The architecture of MOC-AE combines anatomical information from the patients scan using an Autoencoder (AE) with information related to a specific pathology using a classification output with the same image descriptor. This combination of goals forces the network to maintain a balance between anatomical and pathological features of the case while maintaining the low cost of the labels being used. The results obtained are compared with those of similar studies and the strengths and limitations of each approach are discussed. The results demonstrate that the proposed algorithm is capable of achieving state-of-the-art results in terms of both the anatomical and tumor characteristics of the recommended cases.