Brain tumors, Parkinson’s disease, Alzheimer’s disease, and other neurological disorders constitute a major worldwide health burden. Early detection and accurate classification are crucial for prompt intervention as well as effective treatment. Traditional methods of diagnosing these diseases, primarily based on clinical evaluation and neuroimaging techniques like MRI and CT scans, often face limitations such as subjectivity, human error, and difficulty in detecting early-stage markers. With graph neural networks (GNNs) emerging as a highly effective tool for understanding complex neuroimaging data, machine learning (ML) and deep learning (DL) techniques have shown significant potential in recent years in overcoming these challenges. The human brain’s intricate network of regions and connections can be represented as a graph naturally, making GNNs ideally suited to model the complex relationships between brain regions. Unlike traditional convolutional neural networks (CNNs), which operate on grid-like data, GNNs process graph-structured data, capturing non-Euclidean relationships and providing insights into subtle patterns that may be missed by conventional methods. This study explores the application of GNNs in the classification and diagnosis of neurological diseases, highlighting their potential to improve early disease detection, predict disease progression, and support personalized treatment plans. GNNs’ ability to integrate multimodal data, such as genetic information and functional neuroimaging, allows for a more comprehensive understanding of disease mechanisms and enhances diagnostic accuracy. However, challenges remain in implementing GNNs, including the need for large-scale annotated datasets, high computational resources, and model interpretability. This study also discusses the future directions for GNNs in clinical practice and their potential to revolutionize neurological disease diagnosis and treatment. Ultimately, GNNs offer a promising path towards more accurate, efficient, and personalized healthcare solutions for neurological diseases.