Physical activity, recreation and competitive development are vital to a Middle School student's growth. At St Stephen's, students in grades 6 to 8 are required to participate in athletics or physical education classes on five days of the seven letter day rotation. Students may choose to participate on an athletic team, in a physical education or Devil's Canyon Wilderness Program class, or in the Soccer Academy or Tennis Academy (at an additional cost). The school year is divided into three seasons with more than 15 different athletic options offered throughout the year. The Middle School athletic program operates under a no-cut policy, and coaches support all levels of athletic ability, from novice to expert.

Physical education classes introduce traditional sport basics in a non­competitive environment in addition to exposing students to select non­traditional activities and games, such as ultimate Frisbee, yoga or pickleball. In addition, the Devil's Canyon Wilderness Program utilizes more than 200 acres of campus trails for hiking and competitive mountain biking. All students are required to participate in the physical education program.