In the quest to enhance the diagnostic accuracy of neural disorders, particularly autism, this paper presents a novel approach for brain region classification using advanced machine learning techniques. The study utilizes the ABIDE and AAL116 atlas datasets, focusing on segmenting and classifying brain regions from resting-state functional MRI (rs-fMRI) images. We propose a three-stage process. In the first stage, data collection and preprocessing are conducted, where rs-fMRI images are preprocessed into SPM12-NIfTI format. The second stage involves the segmentation of brain regions using a Regularized VNet, resulting in the extraction of AAL116 brain region images, which are then split into training, testing, and validation sets. In the third stage, we introduce a custom-designed BRCNet (Brain Region Classification Network), which discriminates between ‘Autism’ and ‘Normal’ classes. Our segmentation methods are rigorously evaluated using metrics such as Dice Score, Recall, and Precision, with the proposed method achieving a Dice Score of 0.985, Recall of 0.962, and Precision of 0.991, surpassing other tested methods like UNet, Active Contour, and Binary Unit. For classification, various methods, including Support Vector Machines (SVM), Decision Trees (DT), and Neural Networks like ResNet, are compared. Our findings demonstrate that ResNet achieves an exemplary performance with an Accuracy of 97.5%, Sensitivity of 96.2%, Specificity of 97.1%, Precision of 97%, and an F-Measure of 97.93%.