Founded in 1956 by dance pioneers Robert Joffrey and Gerald Arpino, the company has earned a reputation for boundary-breaking performances, including its 1987 presentation of Vaslav Nijinsky's The Rite of Spring, which reconstructed the original choreography from the 1913 premiere that was thought to be lost.

In Los Angeles in 1987, the group premiered a reconstructed version of Igor Stravinsky's The Rite of Spring, which they performed many times in the subsequent years.

The expanded ensemble ended its residency in Los Angeles in 1992, and the company moved from New York City to Chicago in 1995, where it remains to this day.

[1] While Joffrey stayed in New York City to teach ballet classes and earn money to pay the dancers' salaries, Arpino led the troupe.

Rebekah Harkness was an important early benefactor and she made international touring possible (Soviet Union, 1963), but in 1964 she and Joffrey parted ways.

Arpino's 1970 rock ballet Trinity was well received; Joffrey revived Kurt Jooss's The Green Table in 1967, followed by revivals of Ashton's Façade, Cranko's Pineapple Poll, Fokine's Petrushka (with Rudolf Nureyev in 1979), Nijinsky's Afternoon of a Faun, also with Nureyev, and Massine's Le Tricorne, Le Beau Danube and Parade.

The Joffrey Ballet appeared in the motion picture Save the Last Dance (2001), when the two protagonists of the story saw the company perform Sea Shadow and Les Présages in Chicago.

Dance experts Millicent Hodson and Kenneth Archer spent 18 years gathering research on the original ballet in order to properly reconstruct it.

The company, consisting of 40 dancers, performs its regular September–May season at the Civic Opera House in Chicago, and engages in several domestic and international tours throughout the year.