The burden of infectious diseases and antimicrobial resistance (AMR) in Africa highlights the critical need for strengthened genomic surveillance capacities that are embedded within the national public health framework. In the East African Community (EAC), this challenge is compounded by limited infrastructure and insufficient workforce capacity in bioinformatics and genomics, particularly within National Public Health Laboratories (NPHLs). This paper describes the implementation of a regional capacity-building initiative based on a multi-phase Training-of-Trainers (ToT) model across six EAC Partner States. Anchored in a One Health framework, the initiative focused on equipping public health professionals within NPHLs with practical skills in pathogen genomics, AMR analysis, and bioinformatics workflows, while also supporting the institutionalization of standardized procedures and tools. Through modular training, in-country cascade sessions, and structured mentorship, the program enabled integration of genomic approaches into public health surveillance activities. Despite infrastructural and operational constraints, the initiative supported measurable gains in applied proficiency, routine use of genomics tools in surveillance tasks, and regional coordination on pathogen data analysis. This case study outlines the program's design, implementation, and observed outcomes, and offers a transferable framework for workforce and systems development in low-resource settings. This experience contributes to ongoing global discussions on equitable genomic surveillance and preparedness by demonstrating how structured, context-specific training can support sustainable adoption of genomics within national public health institutions.