Progressive multifocal leukoencephalopathy (PML) is caused by the JC virus in the setting of chronic immune deficiency. Developing therapy has been challenged by the rarity of the disease as well as the complexity of patients in whom it develops. Several small trials directed at presumptive antiviral therapies have failed to show convincing clinical efficacy. However, the prognosis of PML has evolved from an almost uniformly fatal encephalitis to a disease where a majority of patients survive. This improvement in outlook has been driven by effective immune reconstitution strategies for the underlying disease, most prominently the improved therapy for human immunodeficiency virus and ability to reverse the effects of natalizumab. While a rapid acting and effective antiviral therapy remains a sought for goal, optimal immune reconstitution to control JC virus without causing brain-damaging immune reconstitution inflammatory syndrome (IRIS) currently is the most practical approach to treat PML.