Autism spectrum disorder (ASD) and ASD symptoms are overrepresented among gender-diverse youth across studies. Gender-diverse and ASD youth are at risk for anxiety, but anxiety is unclear among gender-diverse youth with ASD. The Social Communication Questionnaire (SCQ) is a commonly used ASD screener, including in multidisciplinary gender-affirming programs, but scholars have disagreed on the most optimal cut-off score. To date, no study has investigated the sensitivity and specificity of its established cut-off score of 15 with a sample of transgender youth. Gaining more accurate information about the utility of ASD screening tools with gender diverse youth is critical in order to help refer youth to needed services. Among a sample of 325 transgender youth, this study sought to determine an optimal cut-off score for the SCQ, the prevalence of ASD and ASD symptoms, and the relationship between ASD and anxiety within this population. The current study found that a lower cut-off score of 11 yielded optimal sensitivity and specificity (i.e., the best balance of accurately identifying individuals with ASD based on the screener), and analyses found an overrepresentation of ASD (5.2%) and ASD traits (12.1%). Transgender youth with ASD or ASD symptoms had higher anxiety, and all youth perceived themselves as more anxious than their parents. Future research is needed to identify the needs of this population, with particular consideration for the lived experiences of gender diverse and transgender youth.