Background: Despite the potential for ethical violations when research is conducted with conflict-affected populations, there is limited information on how and the extent to which ethical considerations specific to doing research with these populations are integrated into national and international ethics guidelines and, in turn, how these guidelines translate into practice. This study aims to fill this gap by systematically analyzing the existing research ethics guidance of humanitarian donor countries, conflict-affected countries, United Nations (UN) agencies, and funding agencies, as well as ethics reporting in research articles on conflict-affected populations published in peer-reviewed journals. Methods: A review of 32 research ethics guidelines and granting regulations from UN agencies, donor agencies, and governments was conducted, and the reporting of ethics procedures and practices of 498 articles published in peer-reviewed journals was analyzed. Results: Of the reviewed guidelines and regulations, 87.5% did not mention conflict-affected populations, and only one guideline (3.1%) catalogued any of the complexities of conducting research with conflict-affected populations. Among the reviewed published research articles on conflict-affected populations, obtaining ethics approval or a waiver was reported in only 48.2% of articles, and obtaining informed consent was reported in only 46.6% of studies. In the subset of articles that did not report receiving ethics approval, 88.5% were published in journals that required reporting of ethics approval. Conclusions: This study highlighted a gap in current research guidelines and granting regulations on the ethical conduct of research with conflict-affected populations and illustrated the need for such guidance to be integrated into governing documents and research practices. Moreover, this study demonstrated that there is a need for stricter enforcement of reporting requirements by journals to ensure that research with conflict-affected populations meets the required ethical standard. Partnerships among institutional ethics committees, donor agencies, and journals can ensure that the rights of conflict-affected populations are protected.