He attended Kyoto university in 1967, and became close friends with percussionist Tsuchitori Toshiyuki. In 1972 the pair left university, and Toshiyuki went on to work with Peter Brook, while Kondo joined Yosuke Yamashita. In 1978 he moved to New York, and began performing with Bill Laswell, John Zorn, Fred Frith, and Eraldo Bernocchi amongst others. A year later he released his first recording, and toured Europe with Eugene Chadbourne, and collaborated with European musicians such as Peter Brotzman. Returning to Japan, he worked with Ryuichi Sakamoto, Kazumi Watanabe, and Herbie Hancock. In the mid-1980s he began focussing on his own career, blending his avant-garde origins with electronic music, and has collaborated with numerous musicians around the world since then. In 2002 he worked on an international peace festival in Hiroshima after being approached by the Dalai Lama about organizing one. He is a former member of Praxis. Kondo cooperated with Bill Laswell to make the album Inamorata in 2007.
He founded the band Kondo IMA in 1984. Kondo IMA achieved commercial success but moved to Amsterdam to be alone and to start "Blow the Earth" in 1993. They started "Blow the Earth in Japan" in the summer of 2007 and ended in the autumn of 2011. The film Blow the Earth in Japan is his first experience as a film director.
He started the site “Toshinori Kondo Recordings” ( http://tkrecordings.com ), which is the membership site for selling his music downloaded on September 11, 2014.