A calibration procedure is required in motor imagery-based brain-computer interface (MI-BCI) to tune the system for new users. This procedure is time-consuming and prevents na\"ive users from using the system immediately. Developing a subject-independent MI-BCI system to reduce the calibration phase is still challenging due to the subject-dependent characteristics of the MI signals. Many algorithms based on machine learning and deep learning have been developed to extract high-level features from the MI signals to improve the subject-to-subject generalization of a BCI system. However, these methods are based on supervised learning and extract features useful for discriminating various MI signals. Hence, these approaches cannot find the common underlying patterns in the MI signals and their generalization level is limited. This paper proposes a subject-independent MI-BCI based on a supervised autoencoder (SAE) to circumvent the calibration phase. The suggested framework is validated on dataset 2a from BCI competition IV. The simulation results show that our SISAE model outperforms the conventional and widely used BCI algorithms, common spatial and filter bank common spatial patterns, in terms of the mean Kappa value, in eight out of nine subjects.