The blood-brain barrier (BBB) is a dynamic regulatory barrier at the interface of blood circulation and the brain parenchyma, which plays a critical role in protecting homeostasis in the central nervous system. However, it also significantly impedes drug delivery to the brain. Understanding the transport across BBB and brain distribution will facilitate the prediction of drug delivery efficiency and the development of new therapies. To date, various methods and models have been developed to study drug transport at the BBB interface, including in vivo brain uptake measurement methods, in vitro BBB models, and mathematic brain vascular models. Since the in vitro BBB models have been extensively reviewed elsewhere, we provide a comprehensive summary of the brain transport mechanisms and the currently available in vivo methods and mathematic models in studying the molecule delivery process at the BBB interface. In particular, we reviewed the emerging in vivo imaging techniques in observing drug transport across the BBB. We discussed the advantages and disadvantages associated with each model to serve as a guide for model selection in studying drug transport across the BBB. In summary, we envision future directions to improve the accuracy of mathematical models, establish noninvasive in vivo measurement techniques, and bridge the preclinical studies with clinical translation by taking the altered BBB physiological conditions into consideration. We believe these are critical in guiding new drug development and precise drug administration in brain disease treatment.