The constantly evolving human–machine interaction and advancement in sociotechnical systems have made it essential to analyze vital human factors such as mental workload, vigilance, fatigue, and stress by monitoring brain states for optimum performance and human safety. Similarly, brain signals have become paramount for rehabilitation and assistive purposes in fields such as brain–computer interface (BCI) and closed-loop neuromodulation for neurological disorders and motor disabilities. The complexity, non-stationary nature, and low signal-to-noise ratio of brain signals pose significant challenges for researchers to design robust and reliable BCI systems to accurately detect meaningful changes in brain states outside the laboratory environment. Different neuroimaging modalities are used in hybrid settings to enhance accuracy, increase control commands, and decrease the time required for brain activity detection. Functional near-infrared spectroscopy (fNIRS) and electroencephalography (EEG) measure the hemodynamic and electrical activity of the brain with a good spatial and temporal resolution, respectively. However, in hybrid settings, where both modalities enhance the output performance of BCI, their data compatibility due to the huge discrepancy between their sampling rate and the number of channels remains a challenge for real-time BCI applications. Traditional methods, such as downsampling and channel selection, result in important information loss while making both modalities compatible. In this study, we present a novel recurrence plot (RP)-based time-distributed convolutional neural network and long short-term memory (CNN-LSTM) algorithm for the integrated classification of fNIRS EEG for hybrid BCI applications. The acquired brain signals are first projected into a non-linear dimension with RPs and fed into the CNN to extract essential features without performing any downsampling. Then, LSTM is used to learn the chronological features and time-dependence relation to detect brain activity. The average accuracies achieved with the proposed model were 78.44% for fNIRS, 86.24% for EEG, and 88.41% for hybrid EEG-fNIRS BCI. Moreover, the maximum accuracies achieved were 85.9, 88.1, and 92.4%, respectively. The results confirm the viability of the RP-based deep-learning algorithm for successful BCI systems.