University museums have developed their academic identity as research institutions through collecting, preserving, and exhibiting items of cultural and natural heritage. They are closely related to the development of many academic disciplines, such as medical science, natural science, anthropology, archaeology, and history, through their support of education while conducting original research. Simultaneously, university museums have also demonstrated high standards for museum practices. However, the history and data of university museums have not been adequately studied, and recent controversies reveal their vulnerability due to their ownership structure and lack of understanding of their roles and values by their parent organizations. Motivated by the author’s work experience, this study will examine their history and challenges through case studies of diverse university museums. Then, it will discuss how university museums endeavor to accomplish their missions in public service and strategically address their universities’ goals.