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Electroencephalogram (EEG) signals are essential in brain-computer interface systems. Nowadays, these signals are employed in various medical applications. In the past few years, EEG signals gain more attention in security systems to identify users, as these signals are unique for each individual. The current study explores deep learning frameworks for EEG-based user identification. Data from 107 users were considered for the study, which is acquired using 64 channels. Several experimental tests are performed over both convolutional neural network (CNN) and recurrent neural networks (RNN) using a 10-fold cross-validation process to check system effectiveness. In CNN, 1-D Convolutional layer is employed for the processing of EEG signals. In RNN, LSTM and GRU are used to check system accuracy. For performance measure various metrices were considered such as accuracy, precision, recall and kappa score. Acquired results suggest that gated recurrent unit (GRU) outperforms other models in terms of accuracy and complexity both. GRU model has 91.2% accuracy and has three layers only, which reduces the model’s complexity. The training cost is also decreasing due to the low complexity of the model.