John Paul II is considered by some authorities to have helped to end Communist rule in his native Poland and eventually all of Europe.

Realizing the overcrowding in Cardinal Newman to the south and Francis Libermann to the north due to the growing population of Roman Catholics in the West Hill area, the Metropolitan Separate School Board began establishing a high school within the boundaries of St. Thomas More Roman Catholic Church.

On September 6, 1983, the MSSB established Pope John Paul II Catholic Secondary School with the first 135 students in twelve temporary, portable classrooms next to the closed St. Bede.

Until its completion in September 1988, the building now consists of the gymnasia, library, cafeteria, tech shops, and additional classrooms.

Although Pope's current building was opened and blessed in early 1989, 23 portables were placed due to the growing student population.

During the 2015 Pan American Games, St. John Paul II received a newly paved track and hosted the roller speed skating competition.

The school was accredited by the International Baccalaureate Organization in 2002 with its first class of IB Diploma students graduated in 2005.