A recent development in deep learning techniques has attracted attention to the decoding and classification of electroencephalogram (EEG) signals. Despite several efforts to utilize different features in EEG signals, a significant research challenge is using time-dependent features in combination with local and global features. Several attempts have been made to remodel the deep learning convolution neural networks (CNNs) to capture time-dependency information. These features are usually either handcrafted features, such as power ratios, or splitting data into smaller-sized windows related to specific properties, such as a peak at 300 ms. However, these approaches partially solve the problem but simultaneously hinder CNNs' capability to learn from unknown information that might be present in the data. Other approaches, like recurrent neural networks, are very suitable for learning time-dependent information from EEG signals in the presence of unrelated sequential data. To solve this, we have proposed an encoding kernel (EnK), a novel time-encoding approach, which uniquely introduces time decomposition information during the vertical convolution operation in CNNs. The encoded information lets CNNs learn time-dependent features in addition to local and global features. We performed extensive experiments on several EEG data sets—physical human-robot collaborations, P300 visual-evoked potentials, motor imagery, movement-related cortical potentials, and the Dataset for Emotion Analysis Using Physiological Signals. The EnK outperforms the state of the art with an up to 6.5% reduction in mean squared error (MSE) and a 9.5% improvement in F1-scores compared to the average for all data sets together compared to base models. These results support our approach and show a high potential to improve the performance of physiological and non-physiological data. Moreover, the EnK can be applied to virtually any deep learning architecture with minimal effort.