This scoping review examined research publications related to health and/or wellness along with gender among Canadian Indigenous populations. The intent was to explore the range of articles on this topic and to identify methods for improving gender-related health and wellness research among Indigenous peoples. Six research databases were searched up to 1 February 2021. The final selection of 155 publications represented empirical research conducted in Canada, included Indigenous populations, investigated health and/or wellness topics and focused on gender. Among the diverse range of health and wellness topics, most publications focused on physical health issues, primarily regarding perinatal care and HIV- and HPV-related issues. Gender diverse people were seldom included in the reviewed publications. Sex and gender were typically used interchangeably. Most authors recommended that Indigenous knowledge and culture be integrated into health programmes and further research. More health research with Indigenous peoples must be conducted in ways that discern sex from gender, uplift the strengths of Indigenous peoples and communities, privilege community perspectives, and attend to gender diversity; using methods that avoid replicating colonialism, promote action, change stories of deficit, and build on what we already know about gender as a critical social determinant of health.