A 75-year-old man diagnosed with Waldenström macroglobulinemia (WM) complained of neurological symptoms. Baseline F-FDG PET/CT showed diffusely increased radioactivity in the bone marrow and decreased FDG uptake in the right cerebellum. After rituximab-containing immunochemotherapy, the patient had clinically partial response of WM, but the cerebellar lesion was enlarged. Repeated F-FDG PET/CT was similar to the baseline. Ga-pentixafor PET/CT detected residual tumor of WM in occipital bone and cervical lymph nodes, but there was no uptake in the cerebellar lesion. Finally, John Cunningham virus-related progressive multifocal leukoencephalopathy was confirmed.