Parental separation is the state of being separate or termination of cohabitation between a married couple or care givers by mutual agreement or judicial decree. Education is the most important instrument for human resource development. Education is becoming a universal human right and an important component in young children. In this parental separation in Mayangayanga Gomba district has become a stumbling block hindering young children to achieve quality education due to it’s negative outcomes. Parental separation in children’s academic performance is a serious problem in Uganda since long time ago it has been existing in different communities. There is still poor performance in primary schools and we are facing higher dropout rates in Gomba district simply because of parental separation that is leading to poor performance. This study found out causes and effects of parental separation on academic performance of primary pupils in Mayangayanga sub-county Gomba District the study also came out with the interventions to deal with the problem of parental separation in Gomba district. The study was conducted by using qualitative design. Sixty (60) respondents were involved in the study through interview and group discussion Among the respondents include 10 teachers, 20 primary pupils, 10 church members, 4 local leaders, 10 single parents, and 6 NGO workers who selected to involve in this study all gave information regarded to the questions on interview. The findings indicated that parental separation in access to academic performance is caused by various factors including death, widowhood, and marital separation. The study also discovered the effects of parental separation on the academic performance of primary pupil. These are luck of discipline in children, low grades, low esteem and emotional problems. The study also established interventions or solutions to deal with parental separation including setting strong government policies to help in guiding parents on how to stay together for the good of their children, offering guidance and counseling in all communities in Mayangayanga Sub-County Gomba District in order to alert and to sensitize parents teaching them about being responsible parents, Professional counselors should be felicitated for both parents and children because children need to know that they are not part of the separation, friendly relationship reassurance when parents create a strong relationship with their children it will eventually reduce the problem of parental separation in Mayangayanga Sub- County Gomba District.