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John Bapst currently offers the following clubs for student participation:
| Art Club | French Club | Photography Club |
| Astronomy Club | Intramural Sports | Sailing Club |
| Band Council | Jazz Improv Club | Student Ambassadors |
| Chamber Ensemble | Jazz Combo | Student Environmental Action Club |
| Chess Team | JB Peppers | Student Senate |
| Civil Rights Team | John Bapst Players | Swedish Exchange Program |
| Concert Choir | Junior Classical League (JCL) | Tai Chi Club |
| Debate Club | Key Club | Technology Club |
| Destination Imagination | Literary Magazine - Passages | Yearbook - Bapstonian |
| Filmmakers' Club | Math Team | |
National Honor Society is a service organization of student leaders selected on the basis of academics, service, character, and leadership.