Catholic architecture of the so-called “Christian century” (1549–1639), the period of evangelization before the ban on Christianity in early modern Japan, has been a relatively unexplored topic. The complete destruction of missionary buildings and the scant documentary evidence have limited scholars’ ability to carry out research. Yet, the critical review of missionary documentation opens up alternative possibilities for study. This paper examines Japan’s missionary architecture by re-surveying the historical record. The paper focuses on the problems the missionaries faced in adapting vernacular buildings even as they aspired to erect churches “in their own way.” It further explores how architecture was used by Catholic missionaries and the Christian faithful to visualize their distinct Catholic identity.