International donors continue to prefer vertical programming over systems strengthening despite the universal health agenda. This study explored Dutch policy and practice towards health systems within sexual and reproductive health and rights‐focused partnerships between the Netherlands Ministry of Foreign Affairs and civil society, through a document analysis, 13 in‐depth interviews and a stakeholder workshop. The findings revealed that partnerships supported the Ugandan health system in unstructured ways and had difficulties finding synergies. To ensure sustained outcomes and respond to the renewed urgency of strong health systems in the face of crises, donors should incorporate systems strengthening as an explicit goal.