Non-traditional physical education (PE) programs may facilitate functional movement patterns and develop fitness and work capacity to facilitate long-term physical activity. This program evaluation study compared changes in body composition, movement competency, work capacity, and fitness for high school students in CrossFit or weight training PE; both classes were hypothesized to improve each area, with greater improvements in the CrossFit class. Students participated in 57 min classes 4 days per week for 9 months. Measures including body composition, movement competencies (squat, lunge, push-up, pull-up, hinge, and brace), work capacity (two CrossFit workouts), and fitness (air squats, push-ups, inverted row, plank hold, horizontal and vertical jumps, 5 rep max back squat and press, 500 m bike, and 12 min run) were taken at baseline, midpoint, and post-test. Focus groups to assess students’ experiences and outcomes were conducted at post-test. Students significantly improved in movement competencies (ps= 0.034 to <0.001), work capacity (ps< 0.001), and all fitness tests (ps= 0.036 to <0.001). The CrossFit class was only superior on the 500 m bike. Four themes were identified from the focus groups: (1) increased self-confidence, (2) health improvements, (3) newfound community, and (4) translational sports improvements. Future research should examine changes using an experimental design.