This research aims to reconsider the meaning of education in museums exhibiting difficult histories by analyzing their exhibition utilizing Julia Rose’s (2016) commemorative museum pedagogy (hereafter, CMP). Five museums in Japan were analyzed based on the “5R” (Reception, Resistance, Repetition, Reflection, and Reconsideration) of CMP, which is the response pattern of visitors at the museums, and the “toolbox” (Other, Face, Real, and Narrative) of CMP, which is a collection of tools that the museums utilize to deliver their message to their visitors and that visitors can use to create their ethical representation of the difficult histories. The result shows that the case museums in Japan effectively delivered their messages to their visitors; however, they did not provide enough opportunities for visitors to critically understand the exhibition of the difficult histories. Although the museums played educational roles in a society by suggesting the excavation of unheard voices and stressing the importance of living alongside others with different narratives focused on social justice, they can expand their educational roles by including the “possibility of criticism” in their exhibitions. In detail, they can intentionally exhibit difficult histories with the nuance that the museum’s exhibition is a way of interpreting history so visitors can critically understand it. Also, the museum can provide educational programs in which visitors can debrief their museum observations and ethically represent their understanding of difficult histories. When designing their programs, museums can utilize CMP and the CMP-based analysis of the five museums from this research as a reference. Finally, other agents, such as schools and education-related NGOs, are utilizing museums as learning materials; by collaborating with them, museums can expand their educational roles further.