In particular, the customs administrations of both countries plan to strengthen digital interoperability, the tracking of goods in transit and the use of electronic permits. Certain new procedures, including those relating to the change of destination of cargoes, must be applied immediately.

On 15 September 2026, the South Sudan Revenue Authority and the Uganda Revenue Authority signed a Memorandum of Understanding (MOU) on customs cooperation.

The scheme concerns in particular the movement of goods on the trade corridor between the two countries and is intended to strengthen the exchange of information between administrations.

The third agreement between the two authorities introduces several areas of cooperation which were not included in the previous arrangements.

It includes interoperability of digital systems, transit trade facilitation, mutual administrative assistance and capacity building.

The application of electronic permits is also one of the new measures, with a goal of better tracking goods to South Sudan.

Both jurisdictions also wish to limit unauthorized diversions and changes in destination of goods in transit.

According to John Musinguzi Rujoki, Commissioner General of URA, the use of electronic permits should allow for better control of goods entering South Sudan and then likely to return to Uganda without paying the corresponding duties and taxes. A new procedure for changing the destination of cargo shall be applied immediately.

The implementation of the agreement will be based on three levels of coordination: a supervisory committee led by the heads of both administrations, technical teams and field operations teams.

The difficulties encountered at border crossings must therefore be returned to the technical teams and then to the supervisory committee. The authorities also plan to strengthen the sharing of customs information and cooperation on the control of goods in transit.