Community climate, defined as the degree of support or safety within a community, has implications for transgender and non-binary youth mental health outcomes. To assess the variation of community climate across California, this paper developed a Community Climate Index measuring structural stigma and transphobia at the unit of incorporated city, constructing this index using eight indicators of climate supportive of transgender and non-binary youth. Principal Components Analysis was used to create a single index representing the variance of climate indicators and high-climate and low-climate communities were defined as those within the highest and lowest quartile of California incorporated cities, respectively. Exploration of communities by climate category discovered that on average, low-climate communities are more likely to have a lower median household income and population than high-climate communities. Communities in rural/micropolitan counties and in regions such as inland Northern California and the San Joaquin Valley were significantly more likely to rank low on the Community Climate Index. Using data on non-binary youth mental health outcomes from the California Healthy Kids Survey, averages for school-district level outcomes by community climate category demonstrated that non-binary youth across 7th, 9th, and 11th grades reported poorer mental health outcomes in low-climate districts compared to their counterparts in high-climate districts, especially symptoms of depression and suicidality. Results of this study demonstrate unique characteristics of cities exhibiting poor community climate for transgender and non-binary youth, and the development of a climate index specific to structural and societal transphobia gives precedent for other measures of transgender-specific community climate in other settings.