Despite refugee children being integrated into the Ugandan education system, learning outcomes of refugee students are alarmingly low, particularly in Science, Technology, Engineering, and Mathematics (STEM) subjects in secondary schools. The underlying reasons for the low achievement in STEM subjects remain inadequately understood, particularly from the perspective of teachers who work directly with refugee learners. Achieving STEM educational equity for refugee students requires that teachers’ voices be considered. This study explored teachers’ experiences of teaching STEM subjects to refugee secondary students in Nakivale refugee settlement in Uganda, with the aim of identifying support mechanisms that promote equitable quality refugee STEM education. Gutierrez’s equity framework, which includes the four dimensions of access, achievement, identity, and power, informed and guided the study. Anchored in the philosophy of constructivism, the study adopted a qualitative approach and used a phenomenology research design. The data were generated with 10 teachers of STEM subjects using semi-structured interviews and were analysed thematically. Findings revealed that STEM teachers face multifaceted challenges across all four equity dimensions, including inadequate target-group-specific instructional material and human resources, limited professional development related to refugee education, negative attitudes of refugee students toward STEM subjects, significant language barriers, and unsupportive family backgrounds. It was concluded that in addition to insufficient instructional resources, refugee STEM instruction and learning are greatly affected by identity factors, including language barriers, unsupportive family backgrounds, and traumatic past experiences. The study recommends increasing the provision of STEM instructional materials and human resources, offering professional development tailored to refugee contexts, strengthening English language support for refugee learners, and the utilisation of practical and competence- based learning strategies.