St. John's Jesuit Academy was started as a pilot program with its first class of 30 seventh and 30 eighth graders during the 2004–2005 school year.

This program also organizes on-campus events for inner-city school children such as the annual Easter and Christmas on campus.

The new Carty Fox Commons now includes a student lounge, food court, and a new book and spirit store.

The School Seal is a modification of the family coat of arms of St. Ignatius Loyola, founder of the Jesuits.

In 2007, the St. John's Jesuit Quiz Bowl team won first place in the Toledo City League and the Northwest Ohio Regional Tournament.

Recently in 2023, the Quiz bowl team again won first place in the Toledo City League and the Northwest Ohio Regional Tournament.

There are "house days" with competition in things varying from basketball, to video games, to tug of war.

Points are also rewarded for things like overall GPA, overall behavior, performance in sport and fun activities, and school spirit.

The Instrumental Department has many other extra-curricular groups including the Jazz Ensemble and the Jazz Machine, a basketball pep band, hockey pep band, the Commencement Wind Ensemble and a pit orchestra for St. John's musicals.

A fall play is also performed annually by the Campion Hall Players inside the school's McQuade Theater.

Productions have ranged from Shakespeare's "Twelfth Night" and "The Taming of the Shrew" to Miller's "The Crucible" and Bradbury's "Fahrenheit 451."

Sports at St. John's include basketball, football, soccer, ice hockey, baseball, track and field, cross country, bowling, lacrosse, swimming, golf, tennis, and rowing.

The Titans won or shared the Toledo City League All Sports Trophy 29 times in 37 years – more than all other schools combined.

The academy offers advanced curricula in math, science, English, social studies and one foreign language consisting of Spanish, Latin, or Chinese.

The number of students and activities increased rapidly, and the space the academy administration offices and rooms occupied became crowded.

Athletics at the academy are extra-curricular and consist of cross country, football, basketball, track, lacrosse, and wrestling.

Most teams participate in the local Catholic sports programs with other private seventh and eighth grades.