This article examines Protestant missionary schools in Korea during the Japanese colonial period (1905–1945) as multifaceted institutions that combined education, religion, and unintended political significance. Although formally apolitical and focused on religious instruction and modern pedagogy, they operated within a colonial context that shaped their broader impact. The study argues that these schools created conditions conducive to the development of Korean national consciousness. The findings indicate that they were not neutral in effect but functioned as arenas of contestation in which compliance, adaptation, and resistance coexisted. Despite efforts to separate religion from politics, their educational environments fostered skills and dispositions later mobilized in nationalist movements, including the March First Movement of 1919. The article concludes that Protestant missionary schools played a complex yet significant role, advancing modernization while simultaneously enabling forms of indirect political activism.