This article sets out to elucidate the role of Japanese Protestants in the education of Koreans during the early twentieth century. Scholarship has often assigned only marginal roles to Japanese Protestants within the history of Japanese imperialism, despite the remarkable success of western missionaries in Korea at the time. As imperial expansion progressed, Japanese Protestants intensified their efforts to take up a leading role in the education of Koreans in colonial Korea and in the metropole wishing to spearhead the assimilation of Koreans. By drawing on the colonial discourses of East Asian unity under Japanese leadership, Protestant churches strove to mediate and facilitate colonial policies in Korea. Yet there were also voices of dissent from prominent Japanese Protestants critical of the assimilation policies implemented by colonial authorities in Korea. This ambivalent stance of Protestantism towards Korea is further complicated by the fact that the Korean Young Men's Christian Association in Tokyo served as an important venue of the Korean Independence Movement. Examining Christian magazines and journals of the time, this paper delves into the contentious debates among Japanese Protestants concerning the Korea Mission and the Japanese government's strategy of assimilation through education.