Background Extensive global research has been conducted to explore the neural mechanisms involved in acupuncture treatment for central nervous system (CNS) disorders. However, there is a lack of bibliometric analysis specifically focusing on functional magnetic resonance imaging (fMRI) studies examining the effects of acupuncture on CNS diseases. Objective This study aims to fill this gap by offering a theoretical framework for the current clinical application and future research directions. It presents a comprehensive overview of the current state, hotspots, and global trends in fMRI studies on therapeutic applications and potential mechanisms of acupuncture for CNS diseases over the past two decades. Methods The publications were analyzed using VOSviewer 1.6.18 and CiteSpace 6.1.R6 software running on the Java platform. All publications were acquired from the Science Citation Index-Expanded of the Web of Science Core Collection. The document types were limited to original articles and review articles, with publication dates spanning from October 24, 2003 to October 24, 2023. Only publications written in the English language were considered for analysis. Results fMRI has the advantages of non-invasiveness, high spatial resolution, and signals directly from neural activity in the brain. Compared to the other three brain imaging techniques, fMRI has the most significant articles on acupuncture treatment for CNS diseases in the past two decades, with a substantial increase. As of October 24, 2023, 227 records of fMRI studies on acupuncture for CNS diseases were identified. Notably, a discernible upward trend exists in this domain's overall number of annual publications. It is worth highlighting that China has emerged as the primary contributor to this field. The five most prominent topics explored in fMRI studies on acupuncture for CNS diseases encompassed the concepts of "acupuncture" "fMRI" "electroacupuncture" "functional connectivity" and "stimulation". Furthermore, the frontier areas of investigation encompassed the topics of "migraine without aura" "ischemic stroke" "prophylaxis" and "randomized controlled trial". Conclusion fMRI studies on acupuncture treatment in CNS diseases have potential applications, and the number of publications on this topic is expected to increase rapidly in future research, which may focus on migraine without aura, ischemic stroke, and randomized controlled trials. fMRI studies of acupuncture for CNS diseases have connected various brain areas, focusing on the default mode network. In addition, strengthening collaboration among different academic groups across countries is imperative.