Nokubi church was designed and built by well known Japanese architect Yosuke Tetsugawa in 1908. The building was his first brick church.
Architectual style of churches back then was in transitional era, shifting from wooden structure to brick. The original shape of the church is still well maintained. It is considered as one of the best church buildings in Japan.
Since the island was uninhabeted, the church had been abandoned and damaged. In 1985, Ojika-cho government decided to preserve the church as a cultural property and passed large budget for the project. The building was completely fixed and has been well maintained.
In March 1989, the church building was registered as a cultural property by Nagasaki prefecture. Then, in 2007, the building was added to the Tentative List of UNESCO World Heritage Site as a part of "Churches and Christian Sites in Nagasaki".

There is the history of suppressed secret Christians of 17 families and their hardship since the anti-Christian policy, behind the establishment of the original Nokubi church.
As a monument of the prayers of the secret Christians the church is still watching over the lost Nozaki settlement from the top of the hill.