Being founded in 2015 on the initiative of the same Educational Institution (I. E. P. Juan Pablo II College), the academy began participating in the second division of the Chongoyape Districtal League, initially with the purpose of having the students of said institution be part of the sports academy, although later the hiring of players and athletes was allowed to achieve sporting excellence in the Copa Perú.

Juan Pablo II College managed to be runner-up in the first division of its district, gaining access to the Provincial Stage of the Copa Perú.

The club was the 2023 Liga Departamental de Lambayeque champion for the first time after defeating Juventud La Joya in the final and qualified for the 2023 Copa Perú.

[1] Juan Pablo II College achieved promotion to Liga 2 for the first time and passage to the semifinals of the Copa Perú after defeating Diablos Rojos (Juliaca) in the quarter-finals.

The home stadium of Juan Pablo II College is Estadio Municipal de la Juventud which is located in Chongoyape, Peru.