Jean-Paul Gauthier helped evaluate a special economic zones (SEZ) strategy for South Sudan in 2006 while serving as a Senior Technical Advisor and SEZ point person for the World Bank. South Sudan had recently signed the Comprehensive Peace Agreement, which allowed it to establish its own democratic government, share oil revenues with Sudan, and set a timetable for full independence. The SEZs would have been intended to concentrate infrastructure provision and establish growth poles for manufacturing and other secondary sectors.

Jean-Paul's work in South Sudan is one of several instances of working on SEZ programs in conflict-affected states.