At John Wollaston, the Health and Physical Education Department provides students with opportunities to develop, enhance, and exhibit attitudes and values that promote a healthy lifestyle. Students from Year 7 to Year 10 follow the WA Curriculum, where they explore attitudes and values for a healthy, active lifestyle and demonstrate behaviours consistent with the prevention of ill-health, personal responsibility for their health and physical activity, respect for social justice principles, and a commitment to personal achievement.

Physical Education classes encourage skill development through participation in a variety of specialized sports. From Year 9, students may choose an elective in Outdoor Recreation, a program designed to foster interaction with the environment through physical challenges while developing leadership skills. In Year 11 and 12, the School offers a Certificate II in Outdoor Recreation and Physical Education Studies General.

Extra-curricular activities are a vital part of life at John Wollaston. House-based swimming, cross-country, and athletics carnivals take place throughout the year, with top-performing students given the opportunity to represent the School in inter-school competitions. Additionally, school teams participate in after-school competitions as part of the cocurricular program.