Islam is a minority religion in Japan. In the absence of official statistics on Muslims in Japan, demographic estimates range from between 70,000 to 120,000 Muslim residents with about 10 percent of that number being Japanese. The majority of estimates of the Muslim population in Japan are around 100,000. According to some sources, there were 30,000 Muslims in Japan in 1982.

In the 14th century, Japan was contacted by Islam via merchants from Arab countries and China. Another important contact was made in 1890 when the Ottoman Empire dispatched a naval vessel to Japan for the purpose of starting diplomatic relations between the two empires as well introducing Muslims and the Japanese to each other. This naval vessel, the Ertuğrul, capsized and sank with 609 people aboard, drowning 540 of them, while returning home. In the late 1870s, a biography of the Prophet Muhammad was translated into Japanese. This helped Islam spread and reach the Japanese people. Islam was thought to come to Japan in the early 1900s when Muslim Tatars were escaping Russian expansionism. Hundreds of Tatar Muslim refugees from Central Asia and Russia came to Japan during the wake of the October Revolution in the early 1900s. These Muslims were given asylum in Japan and settled in several main cities around Japan, forming small communities. Some Japanese converted to Islam through contact with these Muslims. During World War II, over 100 books and journals on Islam were published in Japan. With the oil crisis years in the 1970s, the Japanese mass media had given space to the Muslim world in general, and the Arab world in particular, after realizing the importance of these countries for the Japanese economy. In the 1960s hundreds of Pakistani and Bangladeshi Muslims migrated to work in Japan and became settled. According to the International Organization for Migration (IOM), the population of foreign workers in Japan has nearly doubled in the last 20 years, reaching more than 2 million at the end of 2011. However, Muslims from Pakistan and Bangladesh increased in the late 1980s as visa waiver programs were introduced by the Japanese government. There are some 60 Muslim communities alive in Japan, 40 of them non-Japanese.

There are many Islamic foundations in Japan including the Islamic Center Japan, Japan Muslim Association, Japan Muslim Peace Federation, Japan Islamic Trust, Islamic Circle of Japan, Tokyo Mosque, Kobe Muslim Mosque, Nagoya Mosque, Kanazawa Muslim Society, Tsukuba Muslim Resident Association, Mie Masjid-Mie Islamic Culture Center, Islamic Culture Center Sendai, Muslim Association of Kitakyush and Tohoku University Muslim Cultural Association. There has been a response to the growing need for a supportive Muslim community in Japan. The organization initially focused on educating its growing membership about Islam, the goal being to adhere to Islamic values in a religiously diverse community.

The first mosque in Japan, the Kobe Mosque, was built in 1935 with the contributions of Indian, Tatar and Japanese financial support. The first mosque in the capital Tokyo and the second mosque of Japan, Tokyo Mosque was built by Tatar migrants escaping the Russian revolution who were the largest Muslim ethnic group in Japan. But in 1983, the Tokyo Mosque was demolished and rebuilt by the Presidency of Religious Affairs of Turkey in two years and opened for worship in 2000. In the 1970, only two mosques existed in the country. Now, there are about 200 mosques and masjids across Japan. Many Muslim communities have plans to build mosques in the near future. There are only five Japanese imams who serve in mosques. There is not a single Muslim elementary or junior high school in Japan. The Otsuka Mosque in Toshima ward plans to register itself as an educational corporation and establish an Islamic school.

Shumei Okawa, the most prominent Islamic scholar in both the Japanese government and academia in the matter of Japanese-Islamic exchange and studies, managed to complete his translation of the Quran in prison while being prosecuted as an alleged war criminal by the victorious Allied forces. The first indirect translation was done a decade prior by Okawa. Toshihiko Izutsu was another prominent figure who was professor emeritus at Keio University and fluent in over 10 languages including French, Persian, Sanskrit, Chinese, Russian and Greek. In 1958, Izutsu completed the first direct translation of the Quran from Arabic to Japanese. This was an important point for Japanese people to understand Islam.

The number of Muslim tourists to Japan has been increasing yearly. However, with the increasing number of Muslim visitors, tourist associations and businesses have ramped up efforts to improve the situation to better cater to Muslim tourists. Halal or Muslim-friendly restaurants can be found at only major airports and a few leading large hotels. Non-Japanese restaurants offering Bangladeshi, Egyptian, Indian, Indonesian, Iranian, Malaysian, Moroccan, Pakistani and Turkish cuisine along with some vegetarian restaurants may also have halal food options. Within this context, Malaysian Prime Minister Najib Razak gave a keynote speech at the round table meeting of the World Islamic Economic Forum Foundation (WIEF) and Alliance Forum Foundation (AFF) in Tokyo. Razak has reached an agreement with Japanese Prime Minister Shinzo Abe to enhance cooperation in areas such as the halal food industry and Islamic finance.