The integration of graph neural networks (GNNs) with brain functional network analysis is an emerging field that combines neuroscience and machine learning to enhance our understanding of complex brain dynamics. The review first briefly introduces the fundamentals of brain functional networks, followed by an overview of Graph Neural Network principles and architectures. The review then focuses on the applications of these networks and address current challenges in the field, such as the need for interpretable models and effective integration of multi-modal neuroimaging data. We also highlight the potential of GNNs in clinical areas such as perimenopausal depression research, demonstrating th... More >