The study examined the challenges faced by Islamic Religious Education (IRE) teachers in secondary schools in Kampala, Uganda. The background provided an overview of the historical development of Islamic education, from its origins in the 7th-10th centuries to the Ottoman and Mamluk periods. It highlighted the significance of education in alleviating poverty and the factors affecting student performance, such as teaching conditions and teacher-student compatibility. The study aimed to investigate the pedagogical implications in teaching Islam, evaluate the role of Muslim organizations in promoting IRE in Kampala secondary schools, and identify the challenges faced by IRE teachers. The research was conducted in Kampala, where 8 secondary schools (6 private and 2 public) that offered IRE were selected. Data was collected through interviews with 10 IRE teachers. The findings revealed several pedagogical challenges, including teacher-centered approaches, lack of teaching aids, and a focus on examination preparation rather than comprehension. Additionally, the study highlighted the limited role of Muslim organizations in supporting IRE in secondary schools. The key challenges identified included inadequate teaching resources, large class sizes, and a lack of specialized training for IRE teachers. The study concluded by recommending a shift towards a more learner-centered approach in IRE teaching, increased involvement of Muslim organizations in supporting IRE, and the provision of specialized training and resources for IRE teachers. These findings aimed to contribute to improving the quality of Islamic religious education in Ugandan secondary schools.