This study was to establish Sudan Peoples'' Liberation Movement/Army (SPLA/M) Education Policy after signing of a Comprehensive Peace Agreement (CPA) in 2005. Education Policies before CPA were in two forms South and North Sudan. The study was to compare the two Policies relating to Girls'' enrolment and retention in Juba. The result shows an increase from 9,555 to 11,953 from 2003 to 2007. This was attributed to change of SPLA/M education Policy from that of government of Sudan. Low enrolment resulted from domestic chores, cultural hindrances and lack of scholastic materials. According to Africa Education Trust 2003; illiteracy rate in South Sudan SS stands at 80%. Some parents believe education in SS favours boys over girls. Since SPLA/M came to power, it had encountered several challenges such as lack of institutional capacity, economic set backs in sharing of the oil revenues with the Government of National Unity (GoNU). To improve girls'' education, GoSS government should put equal opportunities to all. The findings in this study should go a long way to improve government policy on girl-child education by involving all the stakeholders and compulsory basic education for all.