This is a list of Buddhist temples, monasteries, stupas, and pagodas in Japan for which there are Wikipedia articles, sorted by prefecture.

Ehime

• Kanjizai-ji

Fukui

• Eihei-ji

Fukuoka

• Nanzoin
• Shōfuku-ji
• Jōten-ji

Fukushima

• Enichi-ji

Gifu

• Eihō-ji
• Shōgen-ji
• Shōhō-ji

Hiroshima

• Ankoku-ji
• Buttsū-ji
• Myōō-in

Hyōgo

• Antai-ji
• Chōkō-ji
• Engyō-ji
• Hōrin-ji
• Hōun-ji
• Ichijō-ji
• Jōdo-ji in Ono
• Kakurin-ji in Kakogawa
• Sagami-ji
• Taisan-ji in Kobe

Iwate

• Chūson-ji
• Mōtsū-ji

Kagawa

• Motoyama-ji
• Ōkubo-ji
• Sanuki Kokubun-ji
• Yashima-ji
• Zentsū-ji

Kanagawa

• Engaku-ji
• Hōkoku-ji
• Kenchō-ji
• Kōtoku-in
• Sōji-ji

Kōchi

• Chikurin-ji
• Dainichi-ji
• Hotsumisaki-ji
• Kongōchō-ji
• Kōnomine-ji
• Shinshō-ji
• Tosa_Kokubun-ji
• Zenjibu-ji
• Zenrakuji

Kyoto

• Adashino Nenbutsu-ji
• Byōdō-in
• Chion-in (Head temple of the Jōdo-shū Buddhist sect)
• Daigo-ji
• Daikaku-ji
• Daitoku-ji
• Eikan-dō Zenrin-ji (Head temple of the Seizan branch of Jōdo-shū)
• Ginkaku-ji (Temple of the Silver Pavilion)
• Higashi-Honganji (Head temple of the Ōtani-ha branch within the Jōdo Shinshū school)
• Kinkaku-ji (Rokuonji, Deer Garden Temple, Temple of the Golden Pavilion)
• Kiyomizu-dera
• Kōdai-ji
• Kōzan-ji
• Manpuku-ji (Ōbaku temple at Uji)
• Myōshin-ji
• Nanzen-ji
• Ninna-ji
• Nishi-Honganji (Head temple of the Honganji-ha branch within the Jōdo Shinshū school)
• Ryōan-ji
• Saihō-ji
• Sanjūsangen-dō
• Shinnyō-ji
• Tenryū-ji (major temple of the Rinzai school)
• Tōfuku-ji
  • Manju-ji
• Tō-ji

Mie

• Honzan Senju-ji (Head temple of the Takada branch within the Jōdo Shinshū school)

Miyagi

• Zuigan-ji

Nagano

• Anraku-ji
• Zenkō-ji

Nagasaki

• Fukusai-ji
• Sōfuku-ji in Nagasaki

Nagoya

• Arako Kannon

Nara

• Asuka-dera
• Daian-ji
• Gangō-ji
• Hase-dera
• Hōki-ji
• Hokke-ji
• Hōryū-ji
• Kimpusen-ji
• Kōfuku-ji
• Ōminesan-ji
• Murō-ji
• Saidai-ji
• Shin-Yakushi-ji
• Taima-dera
• Tōdai-ji
• Tōshōdai-ji
• Yakushi-ji

Okayama

• Inryō-ji

Osaka

• Shitennō-ji (the first Buddhist and oldest officially administered temple in Japan)

Saitama

• Heirin-ji

Shiga

• Eigen-ji
• Enryaku-ji (Temple complex on a mountain northeast of the city)
• Ishiyama-dera
• Mii-dera

Shizuoka

• Ryūtaku-ji
• Shōgen-ji
• Taiseki-ji

Tochigi

• Rinnō-ji
• Hon-ji Senju-ji

Tokushima

• Anraku-ji
• Byōdō-ji
• Dainichi-ji
• Gokuraku-ji
• Hōrin-ji
• Jizō-ji
• Jōraku-ji
• Jūraku-ji
• Kannon-ji
• Kirihata-ji
• Konsen-ji
• Kumadani-ji
• Onzan-ji
• Ryōzen-ji
• Tatsue-ji
• Yakuo-ji

Tokyo

• Gōtoku-ji
• Kan'ei-ji
• Sengaku-ji
• Sensō-ji (temple complex)
• Shōfuku-ji in Higashimurayama
• Tsukiji_Hongan-ji
• Zōjō-ji

Toyama

• Kokutai-ji

Wakayama

• Chōhō-ji
• Fudarakusan-ji
• Jison-in
• Mount Kōya (temple complex)
  • Kongōbu-ji
• Negoro-ji
• Seiganto-ji

Yamagata

• Yama-dera

Yamaguchi

• Kōzan-ji in Shimonoseki

Yamanashi

• Kōgaku-ji
• Kuon-ji