The functional and structural integrity of the blood–brain barrier is crucial in maintaining homeostasis in the brain microenvironment; however, the molecular mechanisms underlying the formation and function of the blood–brain barrier remain poorly understood. The major facilitator superfamily domain containing 2A has been identified as a key regulator of blood–brain barrier function. It plays a critical role in promoting and maintaining the formation and functional stability of the blood–brain barrier, in addition to the transport of lipids, such as docosahexaenoic acid, across the blood–brain barrier. Furthermore, an increasing number of studies have suggested that major facilitator superfamily domain containing 2A is involved in the molecular mechanisms of blood–brain barrier dysfunction in a variety of neurological diseases; however, little is known regarding the mechanisms by which major facilitator superfamily domain containing 2A affects the blood–brain barrier. This paper provides a comprehensive and systematic review of the close relationship between major facilitator superfamily domain containing 2A proteins and the blood–brain barrier, including their basic structures and functions, cross-linking between major facilitator superfamily domain containing 2A and the blood–brain barrier, and the in-depth studies on lipid transport and the regulation of blood–brain barrier permeability. This comprehensive systematic review contributes to an in-depth understanding of the important role of major facilitator superfamily domain containing 2A proteins in maintaining the structure and function of the blood–brain barrier and the research progress to date. This will not only help to elucidate the pathogenesis of neurological diseases, improve the accuracy of laboratory diagnosis, and optimize clinical treatment strategies, but it may also play an important role in prognostic monitoring. In addition, the effects of major facilitator superfamily domain containing 2A on blood–brain barrier leakage in various diseases and the research progress on cross-blood–brain barrier drug delivery are summarized. This review may contribute to the development of new approaches for the treatment of neurological diseases.