Background: The complexity of malaria and public health policy responses presents social, financial, cultural, and institutional barriers to policymaking at multiple stages in the policy process. These barriers reduce the effectiveness of health policy in achieving national goals. Methods: We conducted a structured literature review to characterize malaria policy barriers, and we engaged stakeholders through surveys and workshops in Kenya, Tanzania, and Uganda. We compared common barriers presented in the scientific literature to barriers reported by malaria policy stakeholders. Results: The barriers identified in the structured literature review differ from those described in policymaker surveys. The malaria policy literature emphasizes barriers in the implementation stage of policymaking such as those posed by health systems and specific intervention tools. Stakeholder responses placed greater emphasis on the political nature of policymaking, the disconnect between research and policymaking, and the need for better intersectoral collaboration. Conclusions: Identifying barriers to effective malaria control activities provides opportunities to improve health and other outcomes. Such barriers can occur at multiple stages and scales. Employing a stakeholder - designed decision tool framework has the potential to improve existing policies and ultimately the functioning of malaria related institutions. Furthermore, improved coordination between malaria research and policymaking would improve the quality and efficiency of interventions leading to better population health.