Gender Focal Persons (GFPs) are commonly recruited by organisations as part of institutional efforts to mainstream gender. Despite their wide usage, these structures often struggle to achieve the intended goals. The underlying factors that explain their limited success are not well understood; yet, this would inform strategies for institutionalising gender in research institutions. This paper traces the genesis and operationalisation of the gender focal person structures in Rwanda and Uganda national agricultural research organisations, to unearth factors influencing their performance. Results presented are based on document reviews and qualitative interviews with scientists, managers, and GFPs in the two organisations. We found that the GFPs hinged on individuals and donors, and operated in an ad hoc manner without streamlined procedures. The structures were not embedded in institutional frameworks, hence their low visibility within the organisations. They were characterized by informality, voluntarism, unclear terms of reference, and accountability frameworks. We conclude that the ineffective performance of the GFPs in both organisations is explained by the informal approach used to establish, operationalise, and nurture them. Institutionalising the structure would require that the pioneering champions and donors successfully negotiate the embedding of GFPs into the mainstream; eventually, guaranteeing allocation of adequate human and financial resources from national budgets, as well as the establishment of accountability systems.