Abstract This study investigated the conflict between constitutional provisions and customary rights of women in Jonglei state- Bor County, South Sudan. The study emerged as a result of gross violation of women’s rights on issues pertaining to marriage and widow inheritance, hence other rights of women such as right to work and participation in public life were excluded from this study. The study consisted of five chapters; chapter one contains problem and its scope, research objectives, research questions, significance of the study and the definition of operational key terms used in this study. Chapter two is about the reviewed literature related to the study, opinion! ideas of experts and authors, the conflict between law and customs at state level, an overview of South Sudan legal system, the present status of customary law, sources of law, an overview of rights of women under the law and the constitution of South Sudan, customary law in Bor County and finally the conflict between the constitution and customary rights of women, Chapter three of the study concerns mainly with methodology used in the study, while chapter four and five chiefly deal with presentation, interpretation, analysis of data, findings, recommendations and conclusions, The study was limited to South Sudan’s legal systems (statutory and customary laws) and as such few studies about customary law in the Africa region were not much included. The study was guided by three specific objectives thus (I) Level of constitutional provisions on the rights of women (II) level of customary provisions on the rights of women (III) the relationship between constitutional provisions and customary provisions on the rights of women. The study employed descriptive correlational survey research design, with a population of 90 respondents, mainly women. The study found out that the level of constitutional provisions on the rights of women is ~ir in general but provision of Article 15 is not fair; the level of customary provisions on the rights of women is also at fair levels. The study found no significant relationship between the level of constitutional provisions on the rights of women and the level of customary provisions on the same. The study recommended that a review of the constitution, particularly Articles 15 and 123 should be done to further strengthen the rights of women. A section 273 of the South Sudan Penal Code 2008 contradicts the vi constitution and therefore the study recommended it to be reviewed. The role of Non Governmental Organizations, though they are not the sole bearers of human rights protection should not be discouraged but such entities should be involved in order to help in the process of promoting and sensitizing respect for human rights and in particular the rights of women and children.