Relations between South Sudan and Uganda are navigating a complex landscape of military alliance and violent confrontation, as recent events highlight a partnership defined by both deep economic interdependence and deadly border disputes.
A fatal clash on july 30, 2025, brought these tensions to a head when at least four soldiers were killed in Uganda's West Nile region. According to reports, the skirmish began after South Sudanese troops crossed into Ugandan territory, established a camp, and refused to leave. The ensuing confrontation resulted in the deaths of one Ugandan soldier and three South Sudanese soldiers. In the aftermath, both nations agreed to an immediate ceasefire and launched a joint investigation into the incident.
This violent exchange is not an isolated event but part of a persistent pattern of border friction. In september 2024, Ugandan troops reportedly entered South Sudanese territory in the Kajo-Keji district and established military camps, prompting calls from Juba for diplomatic negotiations. A joint border demarcation committee is working towards a permanent resolution, with a decision anticipated in 2027, but until then, the poorly defined border remains a significant source of conflict.
Paradoxically, these clashes occurred during a period of strengthened military and political cooperation. In march 2025, Uganda deployed its special forces to Juba, South Sudan's capital, as political tensions escalated between President Salva Kiir and First Vice President Riek Machar. The move was framed as an effort to stabilize the fragile nation and prevent a return to full-scale civil war. Uganda's military chief, Muhoozi Kainerugaba, issued a strong statement of support for President Kiir, warning that any opposition to his government would be considered a declaration of war against Uganda.
High-level diplomatic efforts have reinforced this alliance. In april 2025, Ugandan President Yoweri Museveni traveled to Juba to meet with President Kiir. The leaders discussed security, trade, and reaffirmed their commitment to South Sudan's 2018 peace agreement, underscoring Uganda's crucial role in its neighbor's stability.
Underpinning this strategic partnership is a burgeoning economic relationship. In january 2025, Uganda surpassed Kenya to become South Sudan's top export destination, with export earnings reaching $606 million. This economic interdependence provides a powerful incentive for both nations to maintain stable relations, as Uganda is a key trade partner for the landlocked South Sudan.
Despite the official cooperation, underlying frictions persist. In march 2025, a political cartoon in a Ugandan media outlet depicting President Kiir in an unflattering light sparked a diplomatic protest from South Sudan's ambassador, who voiced concerns over negative portrayals that could undermine peace efforts. Historically, the relationship has been further complicated by regional power dynamics, including Uganda's competition with Sudan. Some analysts allege that Uganda has supported armed rebels in Sudan to counter Khartoum's influence and prevent a normalization of relations between Sudan and South Sudan.
In conclusion, the relationship between Kampala and Juba is a delicate balance. While shared economic interests and a strategic desire for regional stability have forged a strong alliance, unresolved border disputes and diplomatic sensitivities continue to fuel conflict. The future of South Sudan–Uganda relations will depend on their ability to manage these competing pressures while navigating a volatile regional political environment.