Brain tumors are one of the most threatening causes of death worldwide. Neuroradiologists widely use Magnetic Resonance Imaging as a golden standard non-invasive imaging method for diagnosing Glioma grades. Brain tumor diagnosis based on radiology images is tedious and highly subjective to intra and inter-observer variability; it adversely affects therapeutic planning. Better medical treatment can be provided relating to similar past cases if relevant images are retrieved from an extensive medical image database. Content-Based Image Retrieval systems are potent image tools for dealing with such massive datasets. In a CBIR system, accurate classification and retrieval of similar pathological images can be effectively automated by utilising Convolutional Neural Network-based feature extraction methods. This paper presents a Content-Based Medical Image Retrieval pipeline on a medical domain using the CNN model for feature extraction and the clustering method used to index the feature map database. The proposed system applies a Multi-level Gain-based feature selection to reduce the dimensionality of the feature vectors obtained from the pre-trained CNN models. The experiment follows five-fold cross-validation on BraTS 2018 and 2020 datasets. The proposed system achieves state-of-the-art MRI brain image retrieval performance with a mean Average Precision and Precision@10 of 98.15% and 97.62%, respectively. The results prove the proposed method’s effectiveness and validate its clinical application.