Universitario Popayán was founded in May 2011, after Centauros Villavicencio moved from Villavicencio to Popayán considering Centauros's huge debts, the refusal of financial support from successive local authorities that deemed it as a feeder club for Deportes Quindío, and the support expressed from the Cauca Department Governorate for a football club in the department's capital city. Despite the fact that the move was made before the start of the Finalización tournament, the club played for the rest of the year under its former name "Centauros" due to legal issues. They were authorized by Coldeportes to use the name "Universitario de Popayán" from the 2012 season onwards. Starting from that season, the club began working in Popayán, as well as forming players in its youth ranks who would go on to play in the Colombian U-19 championships.
The club's history has been marked by the continuous exchange of players with Deportes Quindío (which comes from the Centauros Villavicencio era), given that the club's owner, Hernando Ángel, is also Deportes Quindío's controlling shareholder and chairman.