HIV protease inhibitors (PIs) are the cornerstone of Highly Active Antiretroviral Therapy (HAART). Their antiretroviral potent is attributable to their pharmacokinetic properties. Yet, as the pharmacologic target of HIV PIs is localized within HIV-infected cells, cellular pharmacokinetic properties must also be determined to predict not only efficacy, but also toxicity. In this review, we review recent studies about cellular pharmacokinetics of current marketed HIV PIs, as well as the physicochemical properties of HIV PIs and their drug transporters and enzymes. Additionally, a summary of potential strategies for optimizing cellular pharmacokinetics of HIV PIs and initial ideas to study cellular pharmacokinetics is also discussed. Cellular pharmacokinetics of HIV PIs is an important budding field of research that will significantly influence efficacy and toxicity profiles of these essential drugs, and we hope our review will aid in fundamental knowledge for future research.