In general, Japanese people are not overtly religious, and the society as a whole is very secular. If you subscribe to a religion, however, there is representation available. Select a religion from the table of contents below to jump to that section, with links to each religion's congregation in Japan.
Christianity
Tokyo
Victory Christian Center Japan: https://www.vccjapan.org/
St. Paul International Lutheran Church: http://www.spilchurchtokyo.org/
Tokyo Church of Christ: https://tccnet.org/
Grace City Church: https://www.gracecitychurch.jp/english
Ochanomizu Church of Christ: http://www.ochanomizuco-christ.or.jp/eng/home.html
Tokyo Union Church: http://www.tokyounion.org/
New Life Christian Ministries: http://www.nlcmcjapan.org/home.html
Saint Alban's Anglican-Episcopal Church: http://www.saintalbans.jp/
Japan Assemblies of God: http://www.ag-j.org/church-e/08.html
Congregations in Hokkaido, Tohoku, Kanto, Kansai, Shikoku, and Kyushu
Japan Evangelical Lutheran Church: http://www.jelc.or.jp/e/
Yokohama (Kanagawa)
Reformed Presbyterian Church of Japan: http://www.yokohamachristchurch.org/
Yokohama International Baptist Church: http://www.yibc.org/
Yokosuka (Kanagawa)
Yokosuka Baptist Church: http://www.ybcjapan.org/index.php
Aichi
Amazing Grace Mission Church Int'l: http://www.amazinggracejp.org/
Hyogo
Reformed Presbyterian Church of Japan: http://reformedpresbyterian.org/congregations/japan
Congregations throughout Japan
Iglesia Ni Cristo: http://iglesianicristo.net/#1
Congregations in Hokkaido, Tokyo, and Fukuoka
The Church of Jesus Christ of Latter-day Saints (Temples): https://www.churchofjesuschrist.org/temples?lang=eng
Hinduism
Tokyo & Osaka
ISKCON New Gaya Japan: http://iskconjapan.com/
Islam
Tokyo
Otsuka Masjid: http://www.islam.or.jp/en/
Asakusa Mosque: http://www.halalmedia.jp/masjid/masjid-darul-arqamasakusa-mosque/ (no official site)
Tokyo Camii & Turkish Culture Center: http://www.tokyocamii.org/
Makki Masjid: http://www.halalmedia.jp/masjid/makki-masjido-hanajaya-mosque/
Arabic Islamic Institute in Tokyo: http://www.aii-t.org/
Fukuoka
Fukuoka Masjid Al Nour Islamic Culture Center: http://www.fukuokamasjid.org/
Hokkaido
Masjid al Noor Otaru: http://www.noormasjid.com/
Ibaraki City (Osaka Prefecture)
Osaka Ibaraki Mosque: http://osakamosque.org/
Kanagawa
Ebina Mosque: http://www.halalmedia.jp/masjid/ebina-masjidebina-mosque/
Kobe
Kobe Mosque (Masjid Kobe) (no official website currently available)
Osaka
Osaka Masjid: http://osakamasjid.info/
Sapporo (Hokkaido)
Sapporo Masjid: http://www.sapporomasjid.com/
Sendai
Islamic Cultural Center of Sendai: http://iccsendai.org/web/en/
Jainism
Tokyo
Tokyo Jain Temple is located in Tokyo. An English website is not currently available — we recommend searching for the latest contact information online.
Judaism
Tokyo
Jewish Community of Japan (JCC Japan): (website currently unavailable — please search online for the latest information)
Chabad Japan: http://www.chabad.jp/
Sikhism
Hyogo
Gurdwara Guru Nanak Darbar: http://www.gurdwarakobejapan.com/