Background: Transgender (trans) youth who identify outside the gender binary are a growing subpopulation. In this article, we document differences in access to gender-affirming health care between binary and non-binary identified trans youth and explore ways of meeting the health needs of non-binary youth within primary care settings. Methods: The Canadian Trans Youth Health Survey is a national online survey of trans youth, 14–25 years, conducted in 2013–2014. Among the 839 participants who responded to gender identity items in the survey, 41% identified as non-binary. We compared demographic, health outcome, and health care access responses between non-binary and binary (trans girls/women and trans boys/men) youth. Results: Non-binary and binary youth were similar in most demographics, including age, geographic distribution, and ethnocultural backgrounds, however a larger proportion (82%) of non-binary youth were assigned female at birth. Older non-binary youth (aged 19–25) were significantly more likely to forego needed healthcare than older binary youth; no significant differences were found between younger (14–18) non-binary and binary youth in foregoing healthcare. Overall, non-binary youth (13%) were significantly less likely than binary youth (52%) to access hormone therapy, but they were more likely than binary youth to report experiencing barriers to accessing hormone therapy when needed. Conclusions: Non-binary trans youth in Canada report challenges in accessing needed gender-affirming healthcare. Primary care providers are well-situated to integrate a broad range of gender-affirming care services into practice in order to address the unique needs of non-binary youth. Future research is warranted to explore experiences of non-binary youth related to barriers to care and to explore how services can be designed and delivered to better meet the needs of non-binary youth seeking gender-affirming primary care.