For women and girls in the borderlands, violence and abuse is particularly prevalent, with minimal protection from state institutions and courts and only limited monitoring by human rights organizations and non-governmental organizations (NGOs). Men and women are affected differently by violent conflict. As a result, the aim of this paper is to investigate the conflict, peace, and security concerns that women and girls face in the Horn of Africa with specific reference to women and girl’s immigrants on the Somalia borderlands. The paper focuses on the stage of transit to safe shelters or havens. There are many protection regimes for women transiting across borderlands, but as a theoretical framework, this study has adopted Galtung’s Framework on Conflict and Violence. The study mainly uses secondary data. Information about the borderlands of Somalia has been gathered from books, journal papers, and policy documents, among others. The paper concludes that there are serious conflicts and protection issues that affect both women and girls in the borderlands of Somalia and that the mechanisms put in place to address them are not adequate. The paper recommends regional, multi-sectoral and the use of local institutions, among others as some of the strategies to deal with these conflicts and protection issues.