The study examined the influence of school infrastructure on retention of students in secondary schools in Bukwo district, eastern Uganda. The study was guided by systems theory. A cross-sectional survey research design was adopted. It involved 10 secondary schools since the intention was to find out whether they have adequate infrastructures which contribute to students’ retention in secondary schools. Purposive sampling technique was used to select 10 headteachers, 32 teachers and 50 students to partake in the study. Interviews, observations and documentary guides were used for data collection. Qualitative data was analyzed thematically. The study revealed that, secondary schools in Bukwo district eastern Uganda have inadequate infrastructures like classrooms, furniture, ventilations and lighting. This was confirmed by the headteachers, teachers and students participated in the study when they reechoed that, infrastructures in Bukwo secondary schools are inadequate. Therefore, inadequate infrastructures negatively affect students’ retention. Further this research concluded that, retention of students is below the expectations of the stakeholders. It also emphasized that, adequate infrastructures positively impact the retention of students in secondary schools in Bukwo district eastern Uganda. The study recommended that; the government of Uganda should extend more support to the learning institutions with all the necessary financial aid needed to renovate and establish the infrastructures to boost the retention of learners in secondary schools. School administrators should implement infrastructures reorganization strategies to ensure that, students have adequate space to learn and accommodate diverse learning styles.