A 4-year-old aboriginal boy developed encephalitis due to Murray Valley encephalitis virus (MVE) following an earlier infection with Kunjin virus (KUN). The illness was severe, resulting in cerebral atrophy and profound physical and intellectual disability. The earlier KUN infection complicated his serological profile and delayed antibody responses to MVE. By contrast, the reverse transcriptase-polymerase chain reaction (RT-PCR) assay detected MVE in serum 3 days after the onset of illness and 4 days before the appearance of MVE-specific IgM. We suggest that MVE-specific RT-PCR provides rapid and specific diagnosis of MVE and should be used more widely for the diagnosis of acute viral encephalitis in cases originating from flavivirus endemic areas.