The significance of deep learning techniques in relation to steady-state visually evoked potential- (SSVEP-) based brain-computer interface (BCI) applications is assessed through a systematic review. Three reliable databases, PubMed, ScienceDirect, and IEEE, were considered to gather relevant scientific and theoretical articles. Initially, 125 papers were found between 2010 and 2021 related to this integrated research field. After the filtering process, only 30 articles were identified and classified into five categories based on their type of deep learning methods. The first category, convolutional neural network (CNN), accounts for 70% (n=21/30). The second category, recurrent neural network (RNN), accounts for 10% (n=3/30). The third and fourth categories, deep neural network (DNN) and long short-term memory (LSTM), account for 6% (n=30). The fifth category, restricted Boltzmann machine (RBM), accounts for 3% (n=1/30). The literature’s findings in terms of the main aspects identified in existing applications of deep learning pattern recognition techniques in SSVEP-based BCI, such as feature extraction, classification, activation functions, validation methods, and achieved classification accuracies, are examined. A comprehensive mapping analysis was also conducted, which identified six categories. Current challenges of ensuring trustworthy deep learning in SSVEP-based BCI applications were discussed, and recommendations were provided to researchers and developers. The study critically reviews the current unsolved issues of SSVEP-based BCI applications in terms of development challenges based on deep learning techniques and selection challenges based on multicriteria decision-making (MCDM). A trust proposal solution is presented with three methodology phases for evaluating and benchmarking SSVEP-based BCI applications using fuzzy decision-making techniques. Valuable insights and recommendations for researchers and developers in the SSVEP-based BCI and deep learning are provided.