This study explored the effects of a middle school physical activity intervention for adolescent girls on the executive functioning involved in science learning. The girls, ages 11 to 14, were at risk for low self-esteem, sedentary lifestyle, and poor health outcomes. Executive function stems from interdependent cognitive control processes that influence goal setting and information processing, which complement higher order thinking required for acquiring scientific process skills. A 20-week informal triathlon training program served as the intervention for the treatment girls (n = 29). The comparison group of girls (n = 30) was randomly drawn from a matched sample of students of a similar demographic. Mean comparisons, ANCOVA, and Roy-Bargmann stepdown analysis were used to measure outcomes. The intervention contributed to significant improvement in several executive functions and science achievement. These results suggest that an afterschool program with a physical fitness component may improve the executive functions involved in science learning.