Pilgrimage Tour in Japan
The history of Christianity in Japan is truly unique.
From early missionary work to centuries of prohibition, from hidden faith during the ban to its eventual legalization, Japan’s Christian history has many remarkable chapters.
Join a pilgrimage tour and experience this rich and moving history firsthand.
History of Christianity in Japan
The introduction of Christianity
A.D. 1549 -
The picture of Jesuit missionary Francis Xavier
Christianity was first introduced to Japan in 1549 by the Jesuit missionary Francis Xavier, who arrived from Goa, India, as part of a larger mission to spread Christianity throughout East Asia. He landed in Kagoshima, in the southern part of Japan.
At the time, Japan was in the midst of the Sengoku Period (Warring States era), a time of political fragmentation and constant conflict between feudal lords. The missionaries sought to gain the support of local rulers to aid in their evangelization efforts. Some daimyō (feudal lords), such as Ōmura Sumitada and Arima Harunobu, welcomed Christianity and even converted.
By the late 16th century, Christianity had made significant inroads in Japan, with over 150,000 believers. It influenced not only religious life but also culture, trade, and international relations. Christianity was seen as both a spiritual movement and a symbol of Japan's emerging connections with the West.
However, this period of relative acceptance was short-lived. The rise of powerful rulers like Toyotomi Hideyoshi and Tokugawa Ieyasu led to increasing suspicion of foreign influence, eventually resulting in the ban on Christianity and the beginning of severe persecution.
Prohibition and persecution of Christianity
Late 1500s - Early 1600s
Statue of Martyrdom of 26 Christians in Nagasaki
A picture of Fumie which was used in at that time.
A scene of the fumie at that time
Christianity, which had been growing steadily in Japan since its introduction in the mid-16th century, faced a dramatic shift in the late 1500s and early 1600s. The religion was eventually banned, and believers were severely persecuted.
As Christianity spread, Japan's ruling authorities began to view it as a threat for several reasons:
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Ties to Foreign Powers: Christianity was closely associated with European colonial powers like Portugal and Spain, raising fears that Japan might fall under foreign control.
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Disruption to Social Order: The teachings of Christianity sometimes clashed with traditional religions such as Buddhism and Shinto, creating tensions.
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Religious Conflict: Incidents involving conflicts between Christian converts and Buddhist or Shinto institutions caused unrest.
In 1587, Toyotomi Hideyoshi issued the "Edict of Expulsion of the Jesuits," ordering foreign missionaries to leave Japan. Although this was not a full-scale persecution, it marked the beginning of stricter control over Christianity.
After the Tokugawa shogunate was established in 1603, Ieyasu also viewed Christianity with suspicion. In 1612, he issued a ban on Christianity in Tokugawa-controlled territories, and by 1614, a nationwide prohibition was enacted.
This included:
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The expulsion of missionaries and Christian followers
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The destruction of churches
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A ban on worship and proselytizing
With the ban enforced, Christian believers faced harsh persecution, including torture and execution. One of the most famous examples is:
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The 1597 Martyrdom of 26 Christians in Nagasaki: Twenty-six missionaries and converts were crucified in public as a warning to others.
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The Shimabara Rebellion (1637–38): A revolt by oppressed farmers and Christians in Kyushu was crushed by the shogunate, resulting in tens of thousands of deaths.
Following the rebellion, the Tokugawa regime intensified its crackdown on Christianity through the use of "fumie" (stepping on Christian images) and a network of informants. Suspected Christians were ordered to step on these religious images as a public act to demonstrate that they were not followers of the faith.
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If a person refused to step on the image, it was taken as proof of their Christian beliefs, and they were often arrested, tortured, or executed.
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If they stepped on the image, they were considered to have denied Christianity, whether or not they truly believed.
This practice was particularly common in Nagasaki, a major center of Christian missionary activity. The use of fumi-e continued for more than 200 years, until the ban on Christianity was lifted in the Meiji period.
During the Edo period, Christianity was seen as a direct challenge to national unity and was almost completely eradicated from public life.
Yet, despite the oppression, some believers continued their faith in secret as “Kakure Kirishitan” (Hidden Christians), preserving their beliefs through generations.
Faith Under the Ban — The Era of the Hidden Christians
Virgin Mary in the form of the Buddhist Kannon
Photo by Yomiuri Shimbun online
Even after Christianity was officially banned and missionaries were expelled from Japan, many believers continued to secretly uphold their faith. These individuals came to be known as “Kakure Kirishitan,” or Hidden Christians.
Hidden Christians were Japanese believers who practiced Christianity in secret during the period of persecution and prohibition. To avoid detection, they outwardly appeared to follow Buddhism or Shintoism, while secretly passing down their Christian faith within families and close communities.
Without access to priests or churches, the Hidden Christians:
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Memorized prayers and conducted rituals themselves
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Adapted religious icons, such as worshiping the Virgin Mary in the form of the Buddhist deity Kannon
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Used Buddhist prayer beads instead of rosaries
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Translated Latin and Portuguese prayers into Japanese, preserving them orally across generations
Their practices often blended Christian beliefs with elements of local religions, forming a unique, syncretic faith.
Hidden Christians were primarily found in regions where Christianity had once flourished, such as:
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Nagasaki Prefecture (e.g., Goto Islands, Hirado, Sotome)
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Amakusa Islands
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And other remote mountainous or coastal areas
These isolated locations allowed them to maintain their faith away from government surveillance.
In 1865, a group of Japanese villagers visited the Ōura Cathedral in Nagasaki and revealed to the French priest, Father Petitjean, that they shared the same faith. This event shocked the global Catholic community — it was the first confirmation that Christianity had survived in Japan in secret for over 200 years.
End of isolation and freedom of religion
1800s -
With the Meiji Restoration in 1868, Japan shifted from the feudal Tokugawa shogunate to a centralized modern state.
As part of its efforts to modernize and gain equal standing with Western powers, the Meiji government actively adopted Western systems and culture—including religious policy reform.
The longstanding ban on Christianity, which had been in place since the early 17th century, was officially lifted in 1873.
Following this, many Christian missionaries from Western countries, especially the United States, France, and the UK, returned to Japan and resumed their evangelism.
For the first time in about 250 years, freedom of Christian belief has been restored in Japan.
Modern Society and Christianity
- Today
Today, less than 1% of Japan’s population identifies as Christian, including Catholics, Protestants, and members of the Orthodox Church. While churches exist throughout the country, regular church attendance is low, even among those who identify as Christian.
In modern Japan, Christianity is often more influential as a cultural and educational force than as a religion of personal faith.
Since the Meiji period, missionaries established many schools in Japan.
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Today, many prestigious private schools and universities have Christian roots, such as Aoyama Gakuin, Doshisha University, Rikkyo University, Kwansei Gakuin, and Ferris Jogakuin.
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Most students are not Christians, but they experience Christian values through chapel services, Bible classes, and school culture.
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Holidays like Christmas and Valentine’s Day, rooted in Christian tradition, are widely celebrated as commercial and seasonal events.
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Many Japanese couples prefer chapel-style weddings, often with no religious affiliation, reflecting the symbolic and cultural appeal of Christianity.
Nagasaki Prefecture, a historical center of Christianity in Japan, still has a relatively high number of Christians. Some families in the region have preserved their Christian faith for generations, even through centuries of persecution.
The "Hidden Christian Sites in the Nagasaki and Amakusa Regions", now a UNESCO World Heritage site, show how Christian faith and local culture coexist.
Many churches are facing challenges such as an aging congregation and the rise of secularism among younger generations. However, churches with growing foreign communities (e.g., from the Philippines, Korea, and Brazil) are becoming more diverse and vibrant. Churches today are also engaging in social welfare, community service, and international aid, playing meaningful roles beyond religious functions.
Nagasaki
Goto Islands
The Goto Islands, located off the western coast of Nagasaki Prefecture, are much more than a scenic island chain — they are sacred ground where the history of persecuted Japanese Christians lives on.
Dozaki Catholic Church
Old Gorin Church
Catholic Kaitsu Church
Kashiragashima Church
Kusuhara Church
Oso Catholic Church
Photos credit: The official GOTO Travel Guide, https://goto.nagasaki-tabinet.com/en
50 churches in 634.11 km²
The Goto Islands are a remote archipelago where Hidden Christians preserved their faith in secret for over two centuries. Today, the islands are dotted with beautiful churches and offer a powerful journey through Japan’s Christian history.
Churches in GOTO Islands
