The Middle School program cultivates skill development, teamwork, fitness, and sportsmanship. Various club sports are also offered during Students in grades 5 and 6 can participate in athletics on a developmental team and all Middle School scholar-athletes have the chance to compete several times throughout the season.
The Ellis Athletic Association (EAA) organizes an active open gym program for students in grades 5–8, where daily games are arranged during Middle School lunch recess. Every student in the Middle School represents either the Green team or the White team. Each Middle School class elects two EAA representatives who assist the faculty sponsor in planning games and keeping score. Teams accumulate points throughout the year in these intramural activities and results are announced at the Middle School Recognition Assembly at the end of the year.
Various club sports are also offered during Middle School activities periods. Recent club offerings have included ultimate frisbee, softball, soccer, volleyball, and basketball.