Mission Prep has sport programs for: football, cross country running, tennis, softball, volleyball, basketball, soccer, golf, swim and dive, track and field, and baseball.

Mission Prep is frequently in the CIF playoffs, holding many banners for basketball, volleyball, soccer, and cross country running.

In November 2017, a student accused a school administrator of assault and placing them in a carotid chokehold from behind.

The local police department sent a report of the incident to the district attorney's office for review.

[3] In April 2018, the San Luis Obispo County District Attorney declined to indict the administrator.

[4] Every year a majority of the incoming freshmen hike up Cerro San Luis to repaint the giant cement M on the mountain's east face.