Nephrolithiasis is a known side effect of indinavir sulfate, a protease inhibitor used in the treatment of human immunodeficiency virus (HIV). The duration of its side effects, however, has not been well defined. We present a case where a patient presented with symptomatic indinavir-induced nephrolithiasis 3.5 years after discontinuing indinavir. We use this case to illustrate the pathophysiology of indinavir stones and hypothesize how they can occur years after discontinuation by discussing the pharmacokinetics of the drug.