Events in the year 1900 in Japan. It corresponds to Meiji 33 (明治33年) in the Japanese calendar.

• Emperor: Emperor Meiji^[1]
• Prime Minister:
  • Yamagata Aritomo: (until October 19)
  • Itō Hirobumi: (starting October 19)

• Aichi Prefecture: Mori Mamoru
• Akita Prefecture: Takeda Chiyosaburo
• Aomori Prefecture: Munakata Tadashi
• Ehime Prefecture: Tai Neijro
• Fukui Prefecture: Saburo Iwao then Munakata Tadashi
• Fukushima Prefecture: Arita Yoshisuke
• Gifu Prefecture: Kawaji Toshikyo
• Gunma Prefecture: Furusho Kamon then Nobuchika Ogura
• Hiroshima Prefecture: Asada Tokunori
• Ibaraki Prefecture: Fumi Kashiwada then Chuzo Kono
• Iwate Prefecture: Ganri Hojo
• Kagawa Prefecture: Yoshihara Saburo then Yoshitaro Arakawa then Naokata Suehiro
• Kochi Prefecture: Tadashi Tanigawa then Kinyuu Watanabe
• Kumamoto Prefecture: Tokuhisa Tsunenori
• Kyoto Prefecture: Baron Shoichi Omori
• Mie Prefecture: Kamon Furusha
• Miyagi Prefecture: Kiyoshi Shin then Chikaaki Takasaki then Nomura Masaaki then Motohiro Onoda
• Miyazaki Prefecture: Sukeo Kabawaya then Isamu Sonowaya
• Nagano Prefecture: Oshikawa Sokkichi
• Niigata Prefecture: Minoru Katsumata
• Oita Prefecture: Marques Okubo Toshi Takeshi then Sada Suzuki
• Okinawa Prefecture: Shigeru Narahara
• Osaka Prefecture: Tadashini Kikuchi
• Saga Prefecture: Seki Kiyohide
• Saitama Prefecture: Marquis Okubo Toshi Takeshi
• Shiname Prefecture: Matsunaga Takeyoshi
• Tochigi Prefecture: Hagino Samon then Korechika
• Tokyo: Baron Sangay Takatomi
• Toyama Prefecture: Kaneoryo Gen
• Yamagata Prefecture: Baron Seki Yoshiomi

• May 10 – Prince Yoshihito, the future Emperor Taishō, marries Sadako Kujō.
• June 5 – Kyoto Hosei School, as predecessor of Ritsumeikan University has founded.^{[page needed]}

• January 1 – Chiune Sugihara, diplomat (d. 1986)
• January 2 – Mansaku Itami, film director (d. 1946)
• January 13 – Shimizugawa Motokichi, sumo wrestler (d. 1967)
• January 16 – Kiku Amino, author and translator (d. 1978)
• February 11 – Jōsei Toda, educator and peace activist (d. 1958)
• February 27 – Keiji Nishitani, philosopher (d. 1990)
• March 15 – Kenji Tomiki, aikido and judo teacher (d. 1979)
• June 1 – Noburō Ōfuji, film director and animator (d. 1961)
• July 4 – Ukichiro Nakaya, physicist (d. 1962)
• July 5 – Yoshimaro Yamashina, ornithologist (d. 1989)
• July 16 – Mumon Yamada, Rinzai religious leader (d. 1988)
• July 23 – Prince Kaya Tsunenori (d. 1978)
• August 4 – Nabi Tajima, supercentenarian (d. 2018)
• August 23 – Tatsuji Miyoshi, poet, literary critic, and editor (d. 1964)
• December 24 – Hawayo Takata, teacher and master practitioner of Reiki (d. 1980)

• February 26 – Shinagawa Yajirō, politician (b. 1843)
• August 23 – Kuroda Kiyotaka, second Prime Minister of Japan (b. 1840)