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Abstract Background Until recently onchocerciasis was prevalent in 37 out of 112 districts of Uganda with at least 3.8 million people at risk of contracting the disease, but following the launching of community-directed treatment with ivermectin (CDTI) in 1996 and the adoption of an onchocerciasis elimination policy in 2007, the country has made significant progress in combating the disease. By 2015, interruption of transmission had been achieved in ten of the 17 onchocerciasis foci, but cross-border foci remained particularly problematic, and therefore within the onchocerciasis elimination framework, Uganda embarked upon addressing these issues with its neighbouring countries, namely the Democratic Republic of Congo (DRC) and South Sudan. This paper summarises the experience of Uganda in addressing cross-border issues on onchocerciasis elimination with DRC. Main achievements and lessons learned The key achievements comprise of the adoption of an elimination policy by the Government of Uganda, cross-border meetings, training DRC technical staff and entomological/ epidemiological surveys. The first strategy meeting was held in Kampala in 2008, but the second strategy meeting was not held in Kinshasa until 2013. The involvement of the high-level officials from the Ministry of Health of DRC was critical for the success of the second strategy meeting, and was precipitated by collaboration to control an outbreak of Ebola Virus. Both meetings demonstrated the political commitment of endemic countries and allowed the implementation of a joint action plan. Important steps in establishing a mutually respected elimination targets was agreed on during cross border meetings. The African Programme for Onchocerciasis Control facilitated and funded these initial meetings, thus overcoming some political and financial challenges faced by both countries. This highlighted the need for multilateral organisations such as the Expanded Special Project for the Elimination of Neglected Tropical Diseases in cross-border activities for other Neglected Tropical Diseases. The collaboration between both countries facilitated the training of technical staff from DRC in entomology which facilitated joint cross-border activities to update the epidemiological understanding of onchocerciasis in Beni and Mahagi districts in North Kivu and Ituri Provinces respectively. In Nebbi district, Uganda, 23.7% of crabs were infested by the vector Simulium neavei compared with 6.3% in Mahagi district, DRC. Rapid Epidemiological Assessment (REA) revealed nodule prevalence of 3.2% and onchodermatitis at 26.4% from five villages in DRC. Conclusion Political commitment of both countries and the support from APOC allowed two cross-border meetings which were critical for the implementation of initial cross border activities for onchocerciasis elimination.