The first Europeans to Japan came from Portugal and landed on Kyushu in western Japan in 1542, bringing both gunpowder and Christianity along with them. Some lords, especially on Kyushu, and Japan's upcoming leader Oda Nobunaga welcomed these new visitors for the weapons they brought with them and tolerated the missionaries that came together as part of the package.

The missionaries were eventually successful in converting considerable numbers of people in western Japan, including members of the ruling class. Christianity could be practiced openly, and in 1550, Francis Xavier undertook a mission to Kyoto to seek an audience with the Emperor.

However in 1587, in an era of European conquest and colonization, including in the Philippines near Japan, Toyotomi Hideyoshi issued an edict banning missionaries from the country due to the religion's political ambitions, intolerant behavior towards Shinto and Buddhism, and connections to the sale of Japanese people as slaves overseas. In 1597, Hideyoshi proclaimed a more serious banning edict and executed 26 Christians in Nagasaki as a warning.

Intent to bring Japan under complete control, the succeeding Tokugawa Shogunate further hardened the country's anti-Christian stance, accusing the religion of obstructing the authorities, antisocial behavior and intolerance towards the established religions. After a rebellion on the Shimabara Peninsula that involved many Christians in the late 1630s, thousands of rebels were executed and a full ban on Christianity became strictly enforced. Only small pockets of Christians, known as the "Hidden Christians", continued practicing their religion in secret.

Following the Meiji Restoration, freedom of religion was promulgated and the number of Japanese Christians has been slowly increasing again. Today, about one to two million Japanese are Christians (about one percent of Japan's population), and churches can be found across the country. Many Christians live in western Japan where the missionaries' activities were greatest during the 16th century.

A few Christian customs that have become popular among the non-Christian population in modern-day Japan include Christian wedding ceremonies, where brides wear white wedding dresses and where the couple exchange their vows at wedding chapels.

Events like Valentine's Day and Christmas have developed secular status, and retail marketing for these celebrations contribute to their popularity. Seasonally appropriate gifts and decorations start lining the shelves weeks in advance, and illumination events are held. Note that while commonly celebrated by the populace, Valentine's Day and Christmas are not national holidays in Japan.

The following is a list of tourist sites related to Christianity in Japan:

Amakusa Islands

The isolated location of Amakusa and the fact that the islands are close to where Europeans used to enter Japan in the old days, allowed missionaries to convert many inhabitants and even the local lord to Christianity before the religion was banned in the early Edo Period. Today there are numerous museums and churches spread across the islands which reflect this religious heritage.

Shitsu Church and Ono Church

During the ban on Christianity, several Christians resettled to the remote Sotome coast north of Nagasaki City to practice their religion in secret. When the ban was lifted in the late 1800s, many of them rejoined the Catholic Church and constructed churches with the support of foreign priests.

Kuroshima Church

The isolated Kuroshima Island off the coast of Sasebo was another place where many hidden Christians lived during the ban on Christianity. After freedom of religion had been granted, the local parish erected an impressive, Romanesque-style church in the center of the island's town.

Goto Islands

The remote Goto Island chain was another place where many hidden Christians resided during the Edo Period. After the ban on the religion was lifted, large numbers of churches were built on the islands, especially on the most populated islands of Fukue and Nakadori.

Tsuwano Catholic Church

The Tsuwano Catholic Church in Tsuwano was built in 1931 by a Catholic priest from Germany. The church features tatami mats instead of pews. Next to the church stands a small museum with exhibits related to the Christians who were relocated to and persecuted in Tsuwano in the period between the opening of the country in the 1850s and the granting of freedom of religion in 1873.

Saint Nicolai Church

The Saint Nicolai Church, the main cathedral of the Japanese Orthodox Church, was built in 1891 after Saint Nikolai moved the Orthodox Church headquarters from Hakodate to Tokyo. The current building was reconstructed in 1929 after the original cathedral had been damaged in the 1923 Great Kanto Earthquake. The church has been popular since the Meiji Period for its Byzantine architecture featuring a domed roof and a bell tower.

Stone Church

The Stone Church in Karuizawa is an excellent work of architecture. The artistic stone structure blends flawlessly into the surrounding woods; its appearance like a scene from a fairy tale, inviting people to take a closer look. The church's interior is equally imaginative and charming - the reason why this is a popular venue for weddings. When not used for weddings, the Stone Church is open to the public.

Christ's Grave

Christ's Grave is an unusual site 25 kilometers east of Lake Towada where the purported grave of Jesus Christ lies. The claim is widely regarded as an unfounded legend despite the existence of "ancient religious papers" which explain that Jesus actually fled to Japan where he lived his final years and eventually died.