Girón was initially occupied by the Leoquina culture. During the Inca Empire, the area was known as Pacaybamba, meaning guava tree valley. The name Girón was given to the city by Captain Francisco Hernández Girón during his stay there in 1534. The exact date of the city's founding is unknown, as the relevant documents have been lost. When the Spanish built ranches on the land, its indigenous inhabitants moved away into the surrounding countryside and mountains. During the colonial era, land was concentrated in the hands of the rich, and there was a high level of social stratification.
Girón was first classified as a villa (small town), but in 1814 it was elevated to a canton. A treaty following the 1829 Battle of Tarqui was signed in Girón. The canton of Girón was annexed to the canton of Cuenca in 1854. It was promoted to its own canton again in 1884 and demoted again in 1890, finally becoming a canton in 1897. In 1890, Girón encompassed the parroquias of San Fernando, La Asunción, Nabón, Cochapata, Oña, Pucará and Zhaglli, but later several of these parroquias were promoted to canton status. Today, Girón contains only the rural parroquias of La Asunción and San Gerardo