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Uganda established a National Action Plan for Health Security in 2019, following a Joint External Evaluation (JEE) of International Health Regulations (2005) capacities in 2017. The action plan enhanced national health security awareness, but implementation efforts were affected by limited funding, excess of activities, and challenges related to monitoring and evaluation. To improve implementation, Uganda conducted a multisectoral health security self-assessment in 2021 using the second edition of the JEE tool and developed a 1-year operational plan. From 2017 to 2021, Uganda's composite ReadyScore improved by 20%, with improvement in 13 of the 19 technical areas. Indicator scores showing limited capacity declined from 30% to 20%, and indicators with no capacity declined from 10% to 2%. More indicators had developed (47% vs 40%), demonstrated (29% vs 20%), and sustained (2% vs 0%) capacities in 2021 compared with 2017. Using the self-assessment JEE scores, 72 specific activities from the International Health Regulations (2005) benchmarks tool were selected for inclusion in a 1-year operational plan (2021-2022). In contrast to the 264 broad activities in the 5-year national action plan, the operational plan prioritized a small number of activities to enable sectors to focus limited resources on implementation. While certain capacities improved before and during implementation of the action plan, countries may benefit from using short-term operational planning to develop realistic and actionable health security plans to improve health security capacities.