Junpei Shiina was born in Urawa, Saitama on August 6, 1974. He first began learning the piano at five years of age, and in high school became a part of his school's brass band, learning how to play the drums. In 1998 he began songwriting, and in 1999 won the grand prize at the Sony Music SDN 'The Another Goal '99' auditions. Shiina released his first album, Live, in December 1999 through the Sony Music Japan imprint Knockers Records, later debuting properly under Sony in November 2000 with the Shinichi Osawa-produced single "Sekai". His second single "Mujō" was used as an insert song for the Miho Kanno-starring drama Nisenichi-nen no Otoko Un.
Though Shiina often worked with producers, many of his songs were performed and arranged by himself, with his back-up band the Evil Vibrations: guitarist Ryosuke Nagaoka, drummers Takeshi Hatae and Toshiki Hata, bassist Tomohiko Ohkanda and Soil & "Pimp" Sessions member Tabu Zombie on trumpet. The Evil Vibrations recorded much of his debut album Shiina Junpei, which was released in July 2001. In 2002, Shiina collaborated with his sister Ringo Sheena on three cover duets, beginning with Toto's "Georgy Porgy", which they recorded together as a part of a special unit called Yokoshima, featuring Jumpei Shiina on keyboards and Ringo Sheena on chorus. The siblings both released cover albums in May 2002: Junpei Shiina's, Discover, featured a cover of Roberta Flack and Donny Hathaway's 1972 duet "Where Is the Love" sung with his sister, while Ringo Sheena's, Utaite Myōri: Sono Ichi, featured the pair dueting Marvin Gaye and Tammi Terrell's "The Onion Song" (1969). In addition to his sister, Shiina's album Discover featured collaborations with rapper Twigy, members of Tokyo Ska Paradise Orchestra and singer-songwriter Daisuke Kawaguchi.
In June 2003, Shiina released his second original album Amai Yoru no Kaori, led by the single "Time of Gold", a duet with Ryoko Shinohara used in a Japanese commercial campaign for Canada Dry ginger ale. In 2004, Shiina parted with Sony, after releasing the compilation album Rhodes to Freedom. Two years later, Shiina began to be managed by Kronekodow, his sister's personal management agency, and switched labels to R and C with the single "Zanzō" / "Zero-One". He released his third original album Cruisin' in November 2006. In January 2007, Shiina collaborated with his sister and composer Neko Saito on the song "Kono Yo no Kagiri", which was used as the theme song for the film Sakuran (2007) for which his sister was acting as the musical director for.
In 2008, Junpei Shiina formed the soul and funk band Junpei Shiina & the Soul Force, who later renamed themselves the Dezille Brothers in 2010. After performing at the Rising Sun Rock Festival in 2010, the group released their debut album Dashi no Torikata. In November 2014, Shiina began collaborating with guitarist Tomotaka Imamichi, when they formed the band Hitosarai (ヒトサライ).