CiteSpace software was used to visually analyze the research status and hotspots related to stroke and functional magnetic resonance imaging (fMRI) in the past 20 years. Methods: Using China National Knowledge Infrastructure (CNKI) database as the data source, the authors, research institutions, and keywords of studies related to stroke and fMRI in the past 20 years were analyzed by CiteSpace software. Results: A total of 644 literatures were included. Domestic studies on fMRI in the field of stroke began to appear in 2002, showing a rising wave, and is still a research hotspot today. The most published author was Sun Li-min (Fudan University of Shanghai). The research institutions were mainly universities and affiliated hospitals, which had limitations and lack broader communication and cooperation between institutions and regions. The hot areas of fMRI in stroke research mainly focused on acupuncture treatment of stroke, rehabilitation after stroke, and the treatment and mechanism of hemiplegia and aphasia after stroke. fMRI data analysis methods such as functional connection, functional reorganization, and low-frequency amplitude are frequently used. In addition to subject words, the most active clusters of frequently cited keywords are functional connection, review, motor imagery, acupuncture, and hyperbaric oxygen. Conclusion: The knowledge graph of fMRI and stroke shows that it involves different acupuncture treatment, rehabilitation after stroke, treatment and mechanism of stroke sequelae, fMRI data analysis, and multiple other aspects.