It is crucial to address gender equality and women’s empowerment if fish agri-food systems are to contribute more to food security, nutrition, livelihoods, and poverty reduction. However, systemic gendered inequities and barriers persist, undermining progress toward achieving the UN Sustainable Development Goals. To address this, FISH identified and progressed four pathways to advance gender equality and women’s empowerment in fish agri-food systems. Pathway 1: Gender equity considerations must be integrated into every stage of innovation development, dissemination and uptake. This involves moving beyond male-focused innovation processes to include explicit assessments of women’s needs and engaging women as innovators. Pathway 2: Inclusive livelihoods and wealth generation, including women’s economic empowerment, require building of enablers, including supportive familial relations and women’s education, strategies to avoid further loss of assets such as social protection, investments in women’s social networks, and equitably engaging women in decision-making at all scales. Pathway 3: Inclusive governance of small-scale fisheries and aquaculture can be achieved by implementing gender-responsive and rights-based policies, closing gender data gaps and amplifying women’s voice and leadership. Pathway 4: Gender-transformative approaches are needed to engage women and men together to address structural barriers, like constraining gender norms and relations, in fish agri-food systems. FISH resources can help researchers and development practitioners focused on fish agri-food systems apply gender and intersectional lenses in their work.