Continuous wave-diffuse optical tomography (CW-DOT) has emerged as a promising non-invasive neuroimaging technique for assessing brain function. Its ability to provide brain mapping with high spatial resolution over traditional functional near-infrared spectroscopy (fNIRS) has garnered significant interest in clinical and cognitive neuroscience. In this review, we critically summarized the hardware, reconstruction algorithms, and applications of CW-DOT for human brain mapping, providing an up-to-date overview and guidelines for future studies to conduct CW-DOT studies. ScienceDirect, PubMed, Web of Science, and IEEE Xplore databases were searched from their inception up to 1 July 2024. A total of 83 articles were included in the final systematic review. The review focused on existing hardware systems, reconstruction algorithms for CW-DOT, and the applications of CW-DOT in both clinical settings and cognitive neuroscience. Finally, we highlighted current challenges and potential directions of CW-DOT in future research, including the absence of standardized protocols and a pressing need for enhanced quantitative precision. This review underscores the sophisticated capabilities of CW-DOT systems, particularly in the realm of human brain imaging. Extensive clinical and neuroscience research has attested to the technique’s anatomical precision and reliability, establishing it as a potent instrument in research and clinical practice.