This article poses questions, challenges, and dilemmas for health system researchers striving to better understand how gender shapes accountability mechanisms, by critically examining the relationship between accountability and gender in health systems. It raises three key considerations, namely that: (1) power and inequities are centre stage: power relations are critical to both gender and accountability, and accountability mechanisms can transform health systems to be more gender-equitable; (2) intersectionality analyses are necessary: gender is only one dimension of marginalisation and intersects with other social stratifiers to create different experiences of vulnerability; we need to take account of how these stratifiers collectively shape accountability; and (3) empowerment processes that address gender inequities are a prerequisite for bringing about accountability. We suggest that holistic approaches to understanding health systems inequities and accountability mechanisms are needed to transform gendered power inequities, impact on the gendered dimensions of ill health, and enhance health system functioning.