St. Agnes School offers a number of extra-curricular activities for students. Each year, students have the opportunity to participate in a large-scale musical production. A number of musical concerts are held for family and community throughout the school year.

Sports are available to students in fourth through sixth grades. St. Agnes cooperates with the Towanda Area School District to offer sports that can not be offered at St. Agnes. There are also intramural programs and clinics held at the school.