Inclusive policies that attend to sexual orientation and gender identity (SOGI) are associated with more supportive school environments for lesbian, gay, bisexual, and transgender (LGBT) youth. We use the 2013–2015 California Healthy Kids Survey (n = 113,148) matched with principal reports of school policies from the 2014 California School Health Profiles to examine differential effects of SOGI-focused policies for LGB and transgender youth. SOGI-focused policies had a direct association with less truancy, and moderated the association between sexual orientation/gender identity and other school outcomes. SOGI-focused policies were associated with more positive experiences and perceptions of school climate for LGB youth and, to a lesser extent, transgender youth. Findings underscore the importance of inclusive policies, especially those that address the unique needs of transgender students.