(1) The majority of Canadian youth are not meeting physical activity guidelines, and more female than male youth are falling short of these recommendations. School programs and policies are a viable strategy to improve youth physical activity. However, they may differentially affect female and male activity. This study aimed to examine school-level differences in physical activity outcomes among male and female students and to explore how school programs and policies associate with school-level physical activity outcomes among females. (2) This study used data from 136 schools participating in year 7 (Y7 2018-2019) of the COMPASS study. Data on school programs and policies and on student physical activity were collected. School-level means and percentages for outcomes were calculated and compared between males and females and the impact of physical activity programs and policies on female physical activity outcomes were examined. (3) More males met the guidelines, achieved more strength training days and physical activity minutes compared to females. The number of female varsity sports, community partnerships and fitness ambassadors were all positively and significantly associated with female physical activity. (4) Supportive physical activity environments fostered by offering varsity sports, establishing community partnerships and positive role models may promote physical activity among female youth.