Brain-computer interfaces (BCI) from electroencephalography (EEG) provide a practical approach to support human-technology interaction. In particular, motor imagery (MI) is a widely-used BCI paradigm that guides the mental trial of motor tasks without physical movement. Here, we present a deep learning methodology, named Kernel-based Regularized EEGNet (KREEGNet), leveled on Centered Kernel Alignment and Gaussian Functional Connectivity, explicitly designed for EEG-based MI classification. The approach proactively tackles the challenge of intra-subject variability brought on by noisy EEG records and the lack of spatial interpretability within end-to-end frameworks applied for MI classification. KREEGNet is a refinement of the widely accepted EEGNet architecture, featuring an additional kernel-based layer for regularized Gaussian functional connectivity estimation based on CKA. The superiority of KREEGNet is evidenced by our experimental results from binary and multi-class MI classification databases, outperforming the baseline EEGNet and other state-of-the-art methods. Further exploration of our model’s interpretability is conducted at individual and group levels, utilizing classification performance measures and pruned functional connectivities. Our approach is a suitable alternative for interpretable end-to-end EEG-BCI based on deep learning.