Physical Education at Mercy College is based on the principles of physical endeavour and moral integrity. Students are encouraged to work hard, not only to improve their individual performance, but also to understand the positive effects of regular exercise on the body. Learning to cooperate, applying the laws of sportsmanship and competing as part of a team are seen as very important parts of each student's development. Students at Mercy College are taught the necessary physical and social skills that they will be able to utilise during their time at school and continue with into their adult sporting life.

Mercy College delivers a range of competitive and non-competitive learning environments. Walking groups, fitness and weights classes, boules and Frisbee are just some of the areas that students will be able to participate in, in order to develop at their own pace. The College also has specialised soccer classes in Years Eight and Nine, plus a Year Nine Sport and Recreation option where students can surf, play golf, dance, go fishing and learn the arts of kickboxing. The College also teaches the more traditional sports such as soccer, football, tennis, cricket, volleyball, badminton, touch rugby, netball and basketball. All staff within the Physical Education Department strive to ensure that physical activity is an enjoyable and rewarding experience.
Coordinated by Ms Renee Nisbet, teams from Mercy College compete in the North Western Associated Schools competition (NWAS), which provides after-school sporting competition. As a member of the Associated and Catholic Colleges (ACC), Mercy College’s students are also able to participate in athletics, swimming and lightning carnivals.
Mercy College also offers TEE and TAFE pathways in Outdoor Education and Physical Education Studies and has a Health Program that helps Year Eight and Nine students to develop socially and morally.

In the Junior Learning Centre students are involved in an enjoyable daily fitness programme to increase awareness of a healthy lifestyle. They also participate in a physical education programme that focuses on participation and skill development.

The Middle Learning Centre Physical and Health Education Programme focuses on students taking responsibility for their physical activity in Sports Education, where the students run their own tournaments. This allows students to develop their leadership, interpersonal and self management skills in an enjoyable non threatening environment while learning the skills of the game.

There is also an extensive school programe of lunchtime activities, which caters for all students, focusing on maximum participation and enjoyment.