IntroductionAlthough women’s health is prioritised in global research, few studies have identified structural barriers and strategies to promote female leadership and gender equality in the global health research workforce, especially in low-income and middle-income countries.MethodsWe conducted a mixed-methods study to evaluate gender equality in the mental health research workforce in Nepal. The scoping review assessed gender disparities in authorship of journal publications for Nepal mental health research, using databases (PsycINFO, PubMed, Web of Science, NepJol, NepMed) for 5 years. Qualitative interviews were conducted with 22 Nepali researchers to identify structural barriers limiting women’s leadership.ResultsOf 337 articles identified, 61% were by Nepali first authors. Among Nepali first authors, 38.3% were women. Nepali women had half the odds of being first authors compared with men, when referenced against non-Nepali authors (OR 0.50, 95% CI 1.30 to 3.16). When limiting publications to those based on funded research, the odds were worse for first authorship among Nepali women (OR 0.37, 95% CI 0.19 to 0.71). The qualitative analysis supported the scoping review and identified a lack of gender-friendly organisational policies, difficulties in communication and mobility, and limited opportunities for networking as barriers to women’s leadership in global health research.ConclusionEfforts are needed for greater representation of Nepali women in global mental health research, which will require transformative organisational policies to foster female leadership. Those in leadership need to recognise gender inequalities and take necessary steps to address them. Funding agencies should prioritise supporting organisations with gender equality task forces, policies and indicators.