Construction of the original Urakami Cathedral, a brick Romanesque building, began in 1895, after a long-standing ban on Christianity was lifted.
In 1865, the French priest Bernard Petitjean discovered that almost all the Urakami villagers were Christian. Between 1869 and 1873, over 3600 villagers were banished.
During their exile, 650 died martyrs. The persecuted Kakure Kirishitan (Hidden Christians) came back to their home village from 7 years exile in 1873, and decided to construct their own church.
They purchased the land of the village chief where the humiliating interrogations had taken place for two centuries. The annual "fumie" interrogations required those present to tread upon an icon of the Virgin Mary or Jesus. They thought the place was appropriate considering their memory of the long persecution. Construction of the building was started by Father Francine and was completed under the direction of Father Regani. The frontal twin spires stood 64 meters high were constructed in 1875. When completed in 1925 (Taishō 14), it was the largest Catholic church in East Asia.
The atomic bomb that fell on Nagasaki on August 9, 1945 detonated in Urakami only 500 m (1640 ft) from the cathedral, completely destroying it.
A replacement was built in 1959, after a serious debate between Nagasaki city government and the congregation. The city government suggested preserving the destroyed cathedral as a historical heritage, and offered alternate site for a new church.
However, Christians in Nagasaki strongly wanted to rebuild their cathedral on the original place for their historical reasons.
The place is a symbol of the persecution and their suffering. In 1980 it was remodeled to more closely resemble the original French style.
Statues and artifacts damaged in the bombing, including a French Angelus bell, are now displayed on the grounds. The nearby Peace Park contains remnants of the original cathedral's walls. What remained of the cathedral is now on display in the Nagasaki Atomic Bomb Museum.