The purpose of the study was to assess the challenges of school leadership and identify what challenges school leaders face in performing their duties in missionary schools of Yeka Sub city. The study employed a descriptive survey design. In terms, mixed method, where both quantitative as well as qualitative data were combined and analyzed. The unit of analysis for this study was Yeka Sub-city as a sample cluster which has two missionary secondary schools, among which Selam Childrenâ€™s Village and Kebena Adventist School were sampled purposively, while respondents (mainly teachers) were randomly selected from these missionary schools. School principals and educational supervisors were selected using purposive sampling techniques. Data were collected through questionnaire, interview of key informants and observation of the field. Data obtained through questionnaires were analyzed using statistical tools such as frequency count, percentage and mean value. The findings of the study revealed that the sample missionary secondary schools of the sub-city were moderately effective in develop clear and specific plan and encouraging stakeholders in planning and initiate all the concerned bodies to deal with the planning issues of the school. In addition, the research has demonstrated that the overall practice of making clear the school goals and objectives to teachers and students were positive and principal in the sample schools were moderately capable in setting directions and encouraging the staff towards achieving the expected goals. The study has confirmed, the sample schools have moderate ability to evaluate various alternatives and ability to address problems timely. Besides, schools have experienced high rate of turnover of trained managers over the years, school principals are visionary leaders and moderately willingness of principals to take risks and the capacity of preparing plans towards the achievement of expected goals. More specifically, the overall score value, monitoring the use of resources aligned to the academic standards, reviewing the strategies and working guides of resource management in schools were moderate. Finally, it is recommended that the Sub-city and Woreda education offices in collaboration with the Addis Ababa education Biro need to arrange short and long term training to equip the school leaderships with basic knowledge and skills of leading the education sector. Furthermore, it is natural to scale-up the performances of teachers by providing professional development opportunities which ultimately leads to effective instructional process and better performances of the students.