This is a list of number one singles on the Billboard Japan Hot 100 chart in 2009.
| Date | Song | Artist | |
|---|---|---|---|
| January 5 | "Stay with Me" | Kumi Koda | |
| January 19 | "Yume no Tsubomi" | Remioromen | |
| January 26 | "Velonica" | Aqua Timez | |
| February 2 | "Free" | Mao Abe | |
| February 9 | "Yakusoku" | KinKi Kids | |
| February 16 | "Wao!" | Unicorn | |
| February 23 | "One Drop" | KAT-TUN | |
| March 2 | "Milk" | Aiko | |
| March 9 | "Rule" | Ayumi Hamasaki | |
| March 16 | "Believe" | Arashi | |
| March 23 | "Rescue" | KAT-TUN | |
| March 30 | "Wild" | Namie Amuro | |
| April 6 | "One Room Disco" | Perfume | |
| April 13 | "It's All Love!" | Kumi Koda and Misono | |
| April 20 | "Niji" | Kobukuro | |
| April 27 | "Someday" | Exile | |
| May 4 | "Aitai" | Yuzu | |
| May 11 | "Koi no Abo" | NEWS | |
| May 18 | "Ashita ga Kuru Nara" | Juju and Jay'ed | |
| May 25 | "Love Forever" | Miliyah Kato and Shota Shimizu | |
| June 1 | "Keshin" | Masaharu Fukuyama | |
| June 8 | "Ashita no Kioku" | Arashi | |
| June 15 | "Again" | Yui | |
| June 22 | "Haruka" | Greeeen | |
| June 29 | "Spirit" | V6 | |
| July 6 | "Tanpopo" | Yusuke | |
| July 13 | "Everything" | Arashi | |
| July 20 | "Tanabata Matsuri" | Tegomass | |
| July 27 | "Stay" | Kobukuro | |
| August 3 | "Fireworks" | Exile | |
| August 10 | "Ayakashi" | Koichi Domoto | |
| August 17 | "Ichibu to Zenbu" | B'z | |
| August 24 | |||
| August 31 | "Yume o Arigatō" | Yuko Hara | |
| September 7 | "Sotto Kyutto" | SMAP | |
| September 14 | "Niji" | Yuzu | |
| September 21 | "Sono Sake e" | Dreams Come True featuring Fuzzy Control | |
| September 28 | "Blame It on the Girls" | Mika | |
| October 5 | "Yell" | Ikimono-gakari | |
| October 12 | "Colors (Melody and Harmony)" | Jejung and Yuchun | |
| October 19 | "It's All Too Much" | Yui | |
| October 26 | "My Lonely Town" | B'z | |
| November 2 | "Boku wa Kimi ni Koi o Suru" | Ken Hirai | |
| November 9 | "Swan Song" | Kinki Kids | |
| November 16 | "Kyū Jō Show!!" | Kanjani 8 | |
| November 23 | "My Girl" | Arashi | |
| November 30 | "Loveless" | Tomohisa Yamashita | |
| December 7 | "Bandage" | Lands | |
| December 14 | "Nōdōteki Sanpunkan" | Tokyo Jihen | |
| December 21 | "Kimi ni Sayonara o" | Keisuke Kuwata | |
| December 28 | "Hatsukoi" | Masaharu Fukuyama |