(1) School-based physical activity programs such as intramurals provide youth with inclusive opportunities to be physically active, yet we know little about how types of intramurals (e.g., team and individual sports) may contribute to youth MVPA. This research aims to evaluate how real-world changes in types of intramurals available in schools impact youth physical activity over time. (2) This study used three years of longitudinal school- and student-level data from Ontario schools participating in year 5 (2016-2017), year 6 (2017-2018) and year 7 (2018-2019) of the COMPASS study. Data on types of intramural programs from 55 schools were obtained, baseline demographic characteristics were measured and data on physical activity and sport participation were collected on a sample of 4417 students. Hierarchical linear mixed regression models were used to estimate how changes in the type of intramurals associate with youth MVPA over time. (3) Regardless of participation, adding individual and team intramurals was significantly and positively associated with female MVPA in Y6. (4) The indirect, but positive relationship between adding individual and team intramurals and female MVPA may be explained by other characteristics of the school environment that are conducive to female MVPA.