Navigation of drones can be conceivably performed by operators by analyzing the brain signals of the person. EEG signal corresponding to the motor imaginations can be used for generation of control signals for drone. Different machine learning and deep learning approaches have been developed in the state of the art literature for the classification of motor imagery EEG signal. There is still a need for developing a suitable model that can classify the motor imagery signal fast and can generate a navigation command for drone in real-time. In this paper, we have reported the performance of convolutional stacked autoencoder and Convolutional Long short term memory models for classification of Motor imagery EEG signal. The developed models have been optimized using TensorRT that speeds up inference performance and the inference engine has been deployed on Jetson TX2 embedded platform. The performance of these models have been compared with different machine learning models. © 2020, Springer Nature Switzerland AG.