Since the signing of the Comprehensive Peace Agreement (CPA) in 2005, the Ministry of Education, Science and Technology (South Sudan) has been working towards the implementation of a Language and Education Policy in which the mother tongue of the learner is to be used as a medium of instruction for the first three years of primary education. However, with over 63 Southern Sudanese indigenous communities listed in the Interim Constitution, over 50 living languages listed in the Ethnologue and with no recent language survey or assessment done, there are many challenges in terms of language choices for education. The Department of National Languages within the Ministry of Education, Science and Technology has addressed some of these challenges through the running of a series of workshops entitled, "Principles, Practice and Planning for Multilingual Education". This article presents a participatory planning process as well as some of the resulting principles of language choice for implementation of the language policy.