Transgender, non-binary, two-spirit, and other gender non-conforming (GNC) youth have been the focus of increasing scholarly attention over the past decade. A scoping review method was applied to this growing body of literature to identify good practices and important themes in conducting research with GNC youth. A body of non-clinical, English-language scholarship was identified utilizing keywords relating to GNC youth, methods, and methodologies via searches in 33 databases, 3 specific journals, and other online sources. These works were then analyzed for good practices, with themes emerging related to institutional review boards (IRBs) and assent/consent, advisory boards and community involvement, recruitment, identity descriptions, adultism, youth agency and voice, intersectionality, knowledge mobilization, and researcher reflexivity.