This article seeks to examine the consequences of the global war on terror (GWT) in the Horn of Africa. The focus is on the various implications to individual countries and the region as a whole. It therefore, critically interrogates what the consequences are and how they manifested. The interplay between internal and external factors compounding the consequences are critically analysed. Militarisation in the service of geo-strategic and geopolitical interests through creation of division of states into friendly and non-friendly and construction of unholy alliances hinders cooperation and regional integration. The politics of creation of pariah states, related to the GWT, engenders fragility, internal instability, and failed states. This in turn exposes societies to all sorts of pathologies, distorting the process of state and nation formation. The paper interrogates these intertwined variables. The paper contends that the GWT aggravated the precarious state of peace and stability in the Horn region causing far-reaching structural, political, social, economic, security, inter-state relation, integration and diplomatic damages still reverberating even after the GWT has been jettisoned. The study of the consequences of the GWT still remains scanty. The paper hopes to contribute to the dearth of knowledge on the consequence of GWT