Progressive multifocal leukoencephalopathy (PML) is a rare subacute demyelinating disorder of the central nervous system (CNS) caused by the DNA JC human polyomavirus. In immunocompromised hosts, PML is caused by reactivation of a latent infection rather than de novo primary exposure. PML in the setting of hematopoietic cell transplantation (HCT) is exceedingly rare. PML should be considered in the differential diagnosis of HCT recipients, autologous or allogeneic, presenting with worsening of neurological symptoms, especially associated with post-transplant neurodegenerative findings. Although DNA polymerase chain reaction (PCR) of the cerebrospinal fluid (CSF) has emerged as a promising tool for detecting JC virus, a negative result does not rule out PML. Brain biopsy remains the most reliable and accurate method for diagnosing JC virus-associated PML. Presently, there is no universally effective antiviral therapy against JC virus and outcome is fatal in the majority of cases. We hereby describe two cases of PML developing after allogeneic HCT and provide a comprehensive review of the literature.