St. Francis of Assisi welcomes new and experienced runners from grades 3 to 8 to run cross country with our school cross country team. Practices are normally two or three days per week, immediately after school. Students remain on campus and do drills, work on conditioning, and perform timed runs. The goal is to build endurance and have fun. Each year there are two developmental meets and a championship meet. Cross Country takes place from September to November, and the team may continue to run for conditioning in the off-season after school, as well, for those students interested in continuning when the season ends. That off-season schedule varies depending on coach availability.

Students in grades 3 through 8 may go out for Fall  and/or Spring Track. The fall season lasts until November, and there is usally one meet per track season (one in fall, one in spring), normally scheduled on weekends. Spring track takes place from March through May. Track practice is held immediately following the end of school.

Girls volleyball in the fall is open to girls in grades 6 through 8. The school has participated in volleyball for nearly 20 years, and our fall team is currently part of the Virginia Catholic Association Conference (VCAC) league. The program is designed to teach the sport of volleyball, and to instill confidence in players. In the event there are enough players interested, a junior varsity and varsity team will be formed. Games for fall volleyball are held during the week, and practices are normally twice a week immediately following the end of school.

When there is interest, a spring league may be formed at the school through Catholic Youth Organization (CYO), with those spring games occurring only on weekends. The grades for this team are also 6 through 8. A separate spring volleyball clinic is often offered at the school via separate registration, as well as a summer camp, depending on availability and dates. 

In 2022, St Francis of Assisi welcomed its first Judo program to the school. This is a non-league sport, and we are proud to have a talented, experienced Judo instructor available to train the students in grades 1 through 8. Classes are normally held in the evenings on weekdays, and there is a fee for the uniform and Judo Federation registration, but no other costs are extended to students or their families for the training, which makes this program an excellent way for students to try out martial arts! 

Soccer is available for middle school boys in grades 6 through 8 each fall, and for middle school girls in grades 6 through 8 each spring. Teams forming will depend on player and coach availability, and the teams need at least 15 players in order to form. The teams practice after school, and the matches are played against other teams in the Virginia Catholic Association Conference (VCAC) league. Games are held in Prince William, Manassas, Stafford, and Fredericksburg areas. 
Soccer league consists of:

St Thomas Aquinas - Woodbridge
Epiphany - Culpeper
Holy Family - Dale City
Holy Cross - Stafford
Linton Hall - Manassas
St Francis of Assisi
St Patrick - Spotsylvania
St William of York - Stafford