Despite increasing calls to integrate and prioritise sexual and reproductive health (SRH) services in universal health coverage (UHC) processes, several SRH services have remained a low priority in countries' UHC plans. This study aims to understand the priority-setting process of SRH interventions in the context of UHC, drawing on the Malaysian experience. A realist evaluation framework was adopted to examine the priority-setting process for three SRH tracer interventions: pregnancy, safe delivery and post-natal care; gender-based violence (GBV) services; and abortion-related services. The study used a qualitative multi-method design, including a literature and document review, and 20 in-depth key informant interviews, to explore the context-mechanism-outcome configurations that influenced and explained the priority-setting process. Four key advocacy strategies were identified for the effective prioritisation of SRH services, namely: (1) generating public demand and social support, (2) linking SRH issues with public agendas or international commitments, (3) engaging champions that are internal and external to the public health sector, and (4) reframing SRH issues as public health issues. While these strategies successfully triggered mechanisms, such as mutual understanding and increased buy-in of policymakers to prioritise SRH services, the level and extent of prioritisation was affected by both inner and outer contextual factors, in particular the socio-cultural and political context. Priority-setting is a political decision-making process that reflects societal values and norms. Efforts to integrate SRH services in UHC processes need both to make technical arguments and to find strategies to overcome barriers related to societal values (including certain socio-cultural and religious norms). This is particularly important for sensitive SRH services, like GBV and safe abortion, and for certain populations.