Intramurals are an important part of the physical activity offerings in secondary schools; however, it is not well understood how co-ed and gender-specific intramural programs impact intramural participation among male and female students. Therefore, the objective of this research was to examine if the number of co-ed, male-only, and female-only intramurals offered at a school was associated with student participation in intramurals. A large sample of Canadian secondary school students (N = 59,370) completed the COMPASS survey in 2017-2018. School staff reported the number of co-ed, male-only, and female-only intramurals offered at each school. Students reported whether they participated in school intramurals. Hierarchical models were used to assess associations. Intramural participation was marginally higher among male students (36%) than female students (32%; p < 0.0001). Female students attending schools that offered female-only intramurals were 17% (OR 1.17 [95% CI: 1.05-1.30]) more likely to participate. The number of co-ed and male-only intramurals offered were not significantly associated with student participation. We found a positive association between offering female-only intramurals and female intramural participation, highlighting the importance of these programs for female students. Offering female-only intramurals may be a way for schools to improve participation and physical activity levels of female students. More research is needed on the impact of specific sports or activities on male and female student participation.