Stroke is caused by an acute focal disruption of the vasculature in the central nervous system. Neurological-related functional deficits are the most devastating consequences for stroke survivors. Neural signals from stroke patients can reflect the functional statuses of patients and provide insights into the neuronal recovery mechanism for functioning, which could be used as the basis for designing optimal treatment strategies. Near-infrared spectroscopy (NIRS) is a low-cost, noninvasive, easily operated neuroimage method and it is compatible with various rehabilitative programs. These advantages make NIRS an excellent candidate in research for stroke recovery. Here, we focused on the brain functions and recovery for stroke patients at stable status, conducted a systematic literature review about NIRS applications in stroke since 2000 and identified a total of 72 references through ScienceDirect and PubMed database retrieval. The NIRS studies in stroke include resting-state function and its recovery, motor function and its recovery, motor and cognition interference, cognitive function and its recovery, language function and its recovery, emotional function and its recovery and other applications. Based on the results of the quality assessment, we identified some study gaps from the previous research and provided suggestions for some methodological improvement in the future. The trend of NIRS gives a boost to its application in stroke, and the potential research directions for NIRS in stroke are prospected, including multi-center clinical research, treatment efficacy prediction research and brain– muscle coupling research. Finally, limitations of NIRS are discussed.