This study presents a comparative analysis of Early Warning Systems (EWS) in Kenya and Uganda, with a focus on integrating Indigenous Knowledge Systems (IKS) and scientific forecasting to enhance climate resilience in the Karamoja cross-border region. Drawing on 10 key informant interviews with institutional actors and five focus group discussions with indigenous community members, we analyzed community perceptions. While Kenya’s EWS is more technologically embedded and institutionally coordinated, leveraging SMS alerts, satellite data, and county-level governance, Uganda’s system remains more deeply rooted in culturally transmitted, community-led forecasting methods, though elements of formal science are also present. Despite their divergent approaches, both systems face common barriers: limited community feedback, language and literacy gaps, and insufficient recognition of indigenous indicators. Our findings support the development of a hybrid EWS model that combines scientific precision with cultural legitimacy through co-production between meteorological institutions and local knowledge holders. We recommend embedding IKS into national DRM policies, expanding multi-modal dissemination channels, and institutionalizing community feedback mechanisms. By aligning scientific and traditional knowledge systems and strengthening regional coordination, this integrated approach can build trust, improve forecast usability, and promote anticipatory action in vulnerable pastoralist communities. The study contributes to the broader discourse on decolonizing climate governance and emphasizes the importance of inclusive, localized solutions to environmental risk in Sub-Saharan Africa.