Electroencephalography (EEG)-based brain-computer interface (BCI) systems have been extensively used in various applications, such as communication, control, and rehabilitation. However, individual anatomical and physiological differences cause subject-specific variability of EEG signals for the same task, and BCI systems thus require a calibration procedure that adjusts system parameters to each subject. To overcome this problem, we propose a subject-invariant deep neural network (DNN) using baseline-EEG signals that can be recorded from subjects resting in comfortable states. We first modeled the deep features of EEG signals as a decomposition of subject-invariant and subject-variant features corrupted by anatomical/physiological characteristics. Subject-variant features were then removed from the deep features by learning the network with a baseline correction module (BCM) using the underlying individual information in baseline-EEG signals. The subject-invariant loss forces the BCM to assemble subject-invariant features that have the same class, irrespective of the subject. Using 1-min baseline-EEG signals of the new subject, our algorithm can eliminate subject-variant components from test data without the calibration process. The experimental results show that our subject-invariant DNN framework significantly increases decoding accuracies of the conventional DNN methods for BCI systems. Furthermore, feature visualizations illustrate that the proposed BCM extracts subject-invariant features that are close to each other in the same class.