The primary purpose of this study was to assess the academic performance of female students at Kirkos Sub-city primary schools and investigate factors affecting academic achievement of female students. Besides it tried to examine the relationship of academic performance with the major three independent factors, such as, school environment (facilities, teacher competency, and principal leadership); socio-economic status of parents, parental education and sex related factors. For data gathering, both quantitative and qualitative research methods were employed. The techniques used were questionnaires, focus group discussions, and interviews. A pilot study was conducted to assess the clarity of the items, the reliability and the feasibility of the instrument by using 30 students from primary school, who were from similar standard. The questionnaire was administered for 160 grade eight students at Kirkos Sub-City. The qualitative instrument constituted of document analysis, student records, and interview. SPSS 20.0 and Statistical techniques such as Percentage, frequency, Spearman's rho and t-test analysis were used for data analysis. The core results were that female students’ academic performance particularly at primary level (first Cycle) was better than that of male students. On the other hand, the same students, i.e., male students’ academic performance particularly at the second Cycle was better than that of female students. The research has identified that factors, such as, school environment (facilities, teacher competency, and principal leadership); socio-economic status of parents, parental education and sex related factors affected the academic performance of female students. The problems female students encountered were school environment, gender related factors, parental education, and socio-economic factors. In conclusion, the majority of problems female students encounter and 9 those factors that affect female students’ academic performance are school based factors and home based factors. Based on the findings, recommendations were suggested. In this respect school administration is responsible to facilitate school environment and fulfill learning materials that impede female students from achieving better results. The school administration is also expected to encourage parental involvement and work diligently to increase parental interaction at school, attempt to provide legal protection for sexual harassment that prevails in schools, encourage providing progressive gender focused tutorial programmes,