West Nile virus Kunjin subtype (WNV/KUNV) is enzootic across the tropical north of Australia, with epizootic spread into other jurisdictions. The clinical spectrum of illness in humans is poorly described. We report a clinical case of WNV/KUNV encephalitis and performed a retrospective chart audit of all cases of WNV/KUNV notified in the Northern Territory from 1992 to 2010. Thirteen cases of WNV/KUNV disease were identified; case notes were available for 10 of these presentations. Six of these patients had confirmed infection and presented with neuroinvasive illness, whereas the other four suspect cases comprised three cases with arthralgia, myalgia, and/or rash and one case with fever alone. On the available evidence, WNV/KUNV is of lower virulence compared with the New York 1999 strain. Difficulties in serological diagnosis, especially when paired acute and convalescent sera are not available, may adversely impact the accuracy of the epidemiological and clinical understanding of this virus.