Naharin began his training as a dancer with the Batsheva Dance Company. He came to New York one year later at the invitation of Martha Graham to join her company, as well as to make use of a scholarship to the School of American Ballet. After a year with the Martha Graham Dance Company, he continued his studies at The Juilliard School of Music as well as with Maggie Black and David Howard. He then joined the Maurice Béjart Company in Brussels for one season and made his choreographic debut in 1980 in the Kazuko Hirabayashi studio in New York.
From 1980 to 1990 he performed and worked in New York, where he lived with his wife; the dancer Mari Kajiwara who died of cancer in 2001. In 1990 he was appointed Artistic Director of the Batsheva Dance Company.
Naharin's works are performed by many companies throughout the world, including Nederlands Dans Theater, Frankfurt Ballet, Lyon Opéra Ballet, Ballet Nacional d’España (Madrid), Cullberg Ballet (Sweden), and the Opéra National de Paris, among others.
Naharin has been the recipient of many awards and honors, including the Chevalier de l'Ordre des Arts et des Lettres by the French government in 1998, two New York Dance and Performance (Bessie) Awards (for Naharin's Virus at the Brooklyn Academy of Music in 2002 and for Anaphaza at the Lincoln Center Festival in 2003), a Doctor of Philosophy honoris causa by the Weizmann Institute of Science in 2004, and the prestigious Israel Prize for dance in 2005.