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Background: Despite substantial investment in women’s health over the past two decades, and enthusiastic government support for MDG 5 and SDG 3, health indicators for women in Mozambique remain among the lowest in the world. Maternal mortality stayed constant from 2003 to 2011, with an MMR of 408; the estimated HIV prevalence for women of 15–24 years is over twice that for men; and only 12.1% of women are estimated to be using modern contraception. This study explores the perspectives of policy makers in the Mozambican health system and affiliates on the challenges that are preventing Mozambique from achieving greater gains in women’s health. Methods: We conducted in-depth interviews with 39 senior- and mid-level policy makers in the Ministry of Health and affiliated institutions (32 women, 7 men). Participants were sampled using a combination of systematic random sampling and snowball sampling. Participants were asked about their experiences formulating and implementing health policies and programs, what is needed to improve women’s health in Mozambique, and the barriers and opportunities to achieving such improvement. Results: Participants unanimously argued that women’s health is already sufficiently prioritized in national health policies and strategies in Mozambique; the problem, rather, is the implementation and execution of existing women’s health policies and programs. Participants raised challenges related to the policy making process itself, including an ever-changing, fragmented decision-making process, lack of long-term perspective, weak evaluation, and misalignment of programs across sectors. The disproportionate influence of donors was also mentioned, with lack of ownership, rapid transitions, and vertical programming limiting the scope for meaningful change. Finally, participants reported a disconnect between policy makers at the national level and realities on the ground, with poor dissemination of strategies, limited district resources, and poor consideration of local cultural contexts. Conclusions: To achieve meaningful gains in women’s health in Mozambique, more focus must be placed on resolving the bottleneck that is the implementation of existing policies. Barriers to implementation exist across multiple health systems components, therefore, solutions to address them must also reach across these multiple components. A holistic approach to strengthening the health system across multiple sectors and at multiple levels is needed.