Since the end of the Cold War, many internal conflicts have occurred all over the world. In response to these situations aid donors, including the United Nations, governmental aid organizations, and NGOs have implemented many projects to rebuild war-torn societies. However, some of those projects have resulted in having harmful effects on the process of rebuilding societies. This paper argues that even being started with good intentions, some projects without careful consideration of the post-conflict settings can play a role of dividing a society in the long run. In order to examine this point, this paper focuses on the case of Bosnia and Herzegovina and takes up a Japanese aid project carried out in the education sector. In conclusion, this paper emphasizes that peace-building operations must be implemented based on the long-term perspective in order not to do any harm to a postconflict society.