Recurrent droughts, erratic rainfall patterns, and climate-induced livelihood shocks continue to undermine pastoral resilience in the Karamoja Cluster of East Africa. Early Warning Systems (EWS) designed to anticipate drought, rainfall variability, and associated food insecurity have expanded across the region, yet their effectiveness remains constrained by weak integration between scientific forecasting and Indigenous Knowledge Systems (IKS), as well as by institutional and communication gaps. This study presents a comparative analysis of EWS in Kenya and Uganda to examine how Indigenous and scientific forecasting systems coexist, interact, and diverge within transboundary pastoral contexts. Drawing on 10 key informant interviews, five focus group discussions, and policy analysis, the study evaluates differences in indicator systems, dissemination pathways, institutional coordination, trust, and barriers to integration. Findings show that Kenya’s EWS is more technologically embedded and institutionally coordinated, while Uganda’s system remains more culturally embedded and community driven. Despite their differences, both systems face shared challenges, including limited formal feedback mechanisms, language constraints, and insufficient institutional recognition of Indigenous indicators. The study argues that hybrid EWS models that combine scientific precision with cultural legitimacy can enhance trust, usability, and anticipatory action. By clarifying pathways for integration, this research contributes to ongoing efforts to strengthen inclusive and context-responsive climate governance in Sub-Saharan Africa.