Engaging men and boys in sexual and reproductive health and rights (SRHR) and doing so in a way that challenges harmful masculinities, is both neglected and vital for improving the SRHR of both women and men. To address this gap, WHO commissioned a global research priority setting exercise on masculinities and SRHR. The exercise adapted the quantitative child health and nutrition research initiative priority setting method by combining it with qualitative methods. Influenced by feminist and decolonial perspectives, over 200 diverse stakeholders from 60 countries across all WHO regions participated. The exercise forges a collaborative research agenda emphasising four key areas: gender-transformative approaches to men’s and boys’ engagement in SRHR, applied research to deliver services addressing diversity in SRHR among men and women and to generate gender-equality, research designs to support participation of target audiences and reach to policy makers, and research addressing the priorities of those in low-income and middle-income countries.