The type species Unquillosaurus ceibalii was described by Jaime Eduardo Powell in 1979. The generic name is derived from the river Unquillo. The specific name refers to the town El Ceibal.
The holotype, PVL 3670-11, was found at Arroyo-Morterito in the Los Blanquitos Formation dating from the Campanian. It consists of a left pubis, 514 millimetres (1.686 ft) long. The specimen was re-studied by Fernando Novas and Federico Agnolin in 2004, who concluded that the orientation of the pubis had been misinterpreted: it pointed backwards, as was shown by the fossil still being attached to a displaced part of the pubic peduncle of the ilium.
Powell originally assigned Unquillosaurus to the Carnosauria, in 1986. Novas and Agnolin in 2004 concluded from the opisthopubic pelvic anatomy that Unquillosaurus was part of the Maniraptora or at least Maniraptoriformes, and likely closely related to either the Avialae or the bird-like Alvarezsauridae; perhaps it was itself a bird, a basal member of the Metornithes. In 2006 however, Novas stated that Unquillosaurus probably belonged to the maniraptoran clade Dromaeosauridae.