The Paris Foreign Missions Society built the original Sacred Heart church in Yokohama in 1862, in the foreign settlement, immediately after a long-standing ban on Christianity was lifted. It was a brick building with two bell towers. The church moved to its current location in 1906, and the Great Kantō earthquake of 1923 completely destroyed it.
Jan Josef Švagr, a Czech architect, designed the rebuilt church, which was completed in 1933 in the Neo-Gothic style. When the Diocese of Yokohama was erected in 1937, it became the cathedral.
It stands at 44 Yamate-cho, Naka-ku, and is locally known as Yamate Catholic Church. The bishop's seat serves a diocese that includes Kanagawa, Shizuoka, Nagano and Yamanashi prefectures.

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