Abstract: This disclosure relates generally to the field of Electroencephalogram (EEG) classification, and, more particularly, to method and system for EEG motor imagery classification. Existing deep learning works employ the sensor-space for EEG graph representations wherein the channels of the EEG are considered as nodes and connection between the nodes are either predefined or are based on certain heuristics. However, these representations are ineffective and fail to accurately capture the underlying brain's functional networks. Embodiments of present disclosure provide a method of training a weighted adjacency matrix and a Graph Neural Network (GNN) to accurately represent the EEG signals. The method also trains a graph, a node, and an edge classifier to perform graph classification (i.e. motor imagery classification), node and edge classification. Thus, representations generated by the GNN can be additionally used for node and edge classification unlike state of the art methods.