Gender issue becomes one of the serious issues worldwide,because most of the countries in the world especially developing countries and south Sudan in particular,consider the girl child education is less important compared to the boy child education.Since south Sudan is among the most countries that less care about girl‘s learning,girl child in south Sudan deserve the right to education.The purpose of this study was to find out the factors and the ways that have effect on girls‘ learning in senior secondary schools The study have four objectives;To find out those factors and the ways they have effect on girls‘ learning in secondary education in Juba county,to find out how they affect girls‘ learning in senior secondary school in state,to come out with some measures on how to address those factors and their ways of effect on girls‘ learning in secondary school.To take some measures that may help the stakeholders address on those factors affecting girls‘ learning.In this research paper the researcher used qualitative method,which precisely describes the information collected from 40 participants in a narrative way.This was depended on the structured interview and observations as the tools used for data collection.The purposive sampling method was adopted for the data collection process.Purposive sampling technique employed in the selection of students,teachers and parents to ensure that data were collected on the right sources.The major factors affecting girls‘ learning were the problems resulted from family poor economic background,lack of responsibility,domestics work and absent of parents due to social or natural cause.School related problems like lack of sanitary facilities provision for girls‘ health,some bad behaviors among boys and teachers towards girls,distance,textbooks then lack of enough qualify teachers.Then social problems like pregnancies that had occurred many times in the school due relation with unfaithful boyfriends,discrimination of girls,some bad cultural beliefs and some advice from relatives that divert girls‘ interest from learning.Education is the right of every child and a key of transforming life through knowledge experiences.So without education,girls feel denied from the opportunity to develop their full potential and to play a productive and equal role in their families,societies,country and their world.Since the identified factors were negatively affecting girls‘ learning? It is in this light that,the study made a number of recommendations towards the improvement of girl‘ learning in secondary school;the parents,states governments,central government and NGOs should be committed in delivering the necessary supports to attract more girls build confidence in them to pursue their education.Laws should be instituted to ban all bad cultural practices,the necessary teaching and learning materials be provided and monitoring and evaluation team should be put in place to see the girls‘ learning progress.Girls should hold intervention programs that always supported them and wear a positive attitude towards their education.