Thanks to the fast evolution of electroencephalography (EEG)-based brain–computer interfaces (BCIs) and computing technologies, as well as the availability of large EEG datasets, decoding motor imagery (MI) EEG signals is rapidly shifting from traditional machine learning (ML) to deep learning (DL) approaches. Furthermore, real-world MI-EEG BCI applications are progressively requiring higher generalization capabilities, which can be achieved by leveraging publicly available MI-EEG datasets and high-performance decoding models. Within this context, this paper provides a systematic review of DL approaches for MI-EEG decoding, focusing on studies that work on publicly available EEG-MI datasets. This review paper firstly provides a clear overview of these datasets that can be used for DL model training and testing. Afterwards, considering each dataset, related DL studies are discussed with respect to the four decoding paradigms identified in the literature, i.e., subject-dependent, subject-independent, transfer learning, and global decoding paradigms. Having analyzed the reviewed studies, the current trends and strategies, popular architectures, baseline models that are used for comprehensive analysis, and techniques to ensure reproducibility of the results in DL-based MI-EEG decoding are also identified and discussed. The selection and screening of the studies included in this review follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, leading to a comprehensive analysis of 394 papers published between January 1, 2017, and January 23, 2023.