While the acute and collective crisis from the pandemic is over, an estimated 2.5 million people died from COVID-19 in 2022, tens of millions suffer from long COVID and national economies still reel from multiple deprivations exacerbated by the pandemic. Sex and gender biases deeply mark these evolving experiences of COVID-19, impacting the quality of science and effectiveness of the responses deployed. To galvanise change by strengthening evidence-informed inclusion of sex and gender in COVID-19 practice, we led a virtual collaboration to articulate and prioritise gender and COVID-19 research needs. In addition to standard prioritisation surveys, feminist principles mindful of intersectional power dynamics underpinned how we reviewed research gaps, framed research questions and discussed emergent findings. The collaborative research agenda-setting exercise engaged over 900 participants primarily from low/middle-income countries in varied activities. The top 21 research questions included the importance of the needs of pregnant and lactating women and information systems that enable sex-disaggregated analysis. Gender and intersectional aspects to improving vaccine uptake, access to health services, measures against gender-based violence and integrating gender in health systems were also prioritised. These priorities are shaped by more inclusive ways of working, which are critical for global health as it faces further uncertainties in the aftermath of COVID-19. It remains imperative to address the basics in gender and health (sex-disaggregated data and sex-specific needs) and also advance transformational goals to advance gender justice across health and social policies, including those related to global research.