In 2012, Israel deported 500 South-Sudanese refugee children and their families. A year later, a civil war broke out in the young South Sudan and the deportees, along with over one million South-Sudanese citizens, fled to the neighboring Uganda. Since then, many of these children have studied in boarding schools in Uganda. We explore, using qualitative methods, the perceptions and experiences of six Ugandan teachers all working with these children for at least 5 years. The research is unique in studying children who have previously lived and studied in a developed Western environment, and experienced, subsequently, a transition to the global south, with far more conservative social norms and an authoritarian, teacher-centered conception of education. The results show a clear progression in the teachers’ conception of the children, beginning with an impression of the children as rebellious, tending to initiate conflicts, and disrespectful. Gradually, they came to view them as being open and assertive, often very articulate and communicative. They observed changes in the children’s behavior: acquiring language skills, being cooperative with staff, integrating with the other children and caring. Working with the refugee children had a great impact on the teachers’ perceptions and on their personal and professional conduct: they substituted punishments—including physical caning—with other methods of discipline. They endorsed open academic methods based on dialogue in class and between teachers and students, and encouraged experiment-based learning methods. On the other hand, the teachers initial perception of children’s parents as ignorant and disruptive remained unchanged and little effort, if any, was made throughout the years of this educational encounter to include the parents in the educational process. The teachers’ recommendations focused mainly on three issues: preparing the children and the staff to the new experience in order to facilitate integration, enhancing the communication and mutual work with the children’s parents, and giving more attention to the children’s emotional state. The discussion section addresses the limitation of this study, directions for future research, and practical implications.