The scientific name of the long-tailed vole is Microtus longicaudus. The generic name, Microtus, derives from the Greek words μικρός meaning small + οὖς ear. In Latin, the species name longicaudus derives from longus meaning long and cauda meaning tail. The type specimen was a female collected by Vernon Orlando Bailey in the Black Hills at an altitude around near Custer, South Dakota, on July 19, 1887. The description was published by C. Hart Merriam in The American Naturalist the following year. The original scientific name was Arvicola longicaudus. Certain features of the molars were noted, which distinguished the long-tailed vole from other voles known at the time. The species was formerly sometimes regarded as a member of the Old World genus Chionomys.