All classes participate in physical education 30 minutes each day.

They are instructed in a wide variety of sports throughout the school year including: intramural games at lunch time, running club, cross country running, volleyball, basketball, swimming, cross country skiing and downhill skiing.

Students participate in running club at lunch time in the fall.

Grade 1 to 6 students have the option to compete in Nelson city running meets around the city including the district finals at Lakeside Park. Grade 6 to 9 students compete in the West Kootenay Cross Country Meet at Selkirk College, Slocan Pools and other locations around the Kootenays.

St. Joseph students in Grades 5 to 9 can try out for the boy’s and girl’s competitive volleyball teams. There is also a non-competitive coed volleyball team in which all students can join. All teams compete against other intermediate schools around the Kootenay's in October & November.

Basketball is available to students in the winter months. A coed team competes against a number of schools in Nelson. Intermediate students also coach primary students during the Intramural Basketball Club at lunchtime after Spring Break.

The St. Joseph athletic teams have a new look as of the 2021-2022 school year. Go Eagles!