Implementation of the Cluster Approach has been a major recent development in the humanitarian system. The aim of this study was to explore the strengths and weaknesses of the humanitarian Cluster Approach in relation to services for sexual and reproductive health (SRH) [including gender-based violence (GBV)] in northern Uganda, which is recovering from over 20 years of armed conflict. Face-to-face and telephone, semistructured, qualitative interviews were conducted in 2009 with purposively selected key informants from governmental, non-governmental, United Nations and donor agencies working in northern Uganda. Respondents noted a number of contributions of the Cluster Approach, including improved co-ordination of SRH services and stronger advocacy. However, concerns were raised about the low prioritisation, limited leadership and capacity, and standard setting for SRH services. Concerns were also raised about limited planning and capacity for dissolution of the Clusters in the transition to recovery and development in northern Uganda. Despite a number of contributions made by the Cluster Approach, particularly for responding to GBV, there were many concerns about its limited influence on SRH services. There were also concerns that the transition to recovery and development in northern Uganda may not result in reproductive health services being sufficiently strengthened.