The purpose of this study was to explores on the factors affecting academic achievement of the students in secondary schools of Bor Municipal Council, Jonglei State, the study focused on the Senior threes and senior fours outputs in the National examinations in relation to access to University entry and better learned skills, Due to the exploratory nature of the study and the holistic approach that was undertaken, home environment, parents, school environment, Teachers, and Learners factors were targeted as points of the investigation, Multiple methods of data collection were used, first, data was collected through Focused Group Discussion interviews with the learners, teachers, PTAs, and Key Informants interviews with head teachers of the schools and the directors in the directorate of secondary schools, Secondly, an observational method was used to collect the data such as time management by learners and teachers, behavioral patterns inside and outside the classrooms and in the schools compound, Teachers teaching methodologies, school learning facilities inside and outside. Documentary analysis was used to review on the attendance registers of learners and Teachers schemes of work, lesson plans and previous years SSCSE results, data collected was analyzed using contents analysis and the use of Excel spread sheet using tables since the design was qualitative. The key findings of this research revealed that; learners’ environment was not adequately supporting better learning due to the following factors, parents’ low level of education, unemployment rates among the parents, parents over working students after school hours, lack of educational resources at home. In school environment, the study results revealed; poor learning structures, use of use English language as the medium of the instruction in schools, long distance being travelled from home to the schools, poor locations of the learning institutions, lack of setup libraries and laboratories in the school environment, lack of teaching/learning aid in the schools, teacher-learner absenteeism, lack of teachers motivations, students overcrowding and lack of teachers experiences in teaching leading to teacher centered method hence leading to less attentions being paid to the learners with special learning needs, present of unqualified teachers in the schools. Peers group influence among the students in the schools due to low socio-economic status, lack of learners’ motivation and low attitude toward learning among the students. As a result, the study concluded that; Home, Parents, school environment, teachers and learners factors collaborated in producing poor academic achievements of the students at Bor Municipal council secondary schools. Recommendations were made for more attentions to be given to these factors by all the educational stakeholders both National and Privates actors.