Background: Publishing study protocols have been growing recently due to its substantial benefits such as increasing the research transparency, reducing the selective reporting of the outcomes, and preventing unnecessary duplications of the research. Objectives: This paper explains the rationale and methods of a policy analysis study on newborn mortality in Iran. Study objectives are: identifying the risk factors of neonatal mortality in Iran, identifying the experiences of successful countries, analysis of policies of reducing neonatal mortality in Iran, analysis for policies of reducing neonatal mortality in high-burden provinces of neonatal mortality in Iran. Methods: This study has four steps each of which is corresponding to one aim of the study. The steps are: systematic review of the risk factors of neonatal mortality in Iran, comparative study of policy making of reducing neonatal mortality in successful countries, analysis of policies of reducing neonatal mortality in Iran by using policy models, and developing policy options for reducing the neonatal mortality in the high-burden provinces. Conclusion: This study is designed for analysis of the policies of reducing neonatal mortality in Iran and then providing recommendations for the provinces that rank higher in terms of neonatal mortality. The study will identify the successes, failures, and defects of the policies. So, using them, we would be able to develop proper plans for more reductions of the neonatal mortality. Moreover, the findings and methods of this study can help other countries, especially the developing countries, in reducing their neonatal mortality and also in other areas of health such as under-five mortality and maternal mortality.