The 1999 revival had a pre-Broadway engagement from December 29, 1998 to January 24, 1999 at the Kennedy Center in Washington, D.C. Previews began on Broadway on February 2, 1999 at the Marquis Theatre, with an official opening on March 4, 1999, and closed on September 1, 2001 after 35 previews and 1,046 performances.

The revival starred Bernadette Peters as "Annie" and Tom Wopat as "Frank Butler", with direction by Graciela Daniele and choreography by Jeff Calhoun. Peters won the 1999 Tony Award for Best Actress (Musical) and the production won the 1999 Tony Award for Best Revival of a Musical.

This production had a revised book by Peter Stone and new orchestrations, and was structured as a "show-within-a-show", set as a Big Top travelling circus. "Frank Butler" is alone on stage and introduces the main characters, singing "There's No Business Like Show Business", which is reprised when "Annie" agrees to join the traveling Wild West show. The production dropped several songs (including "Colonel Buffalo Bill", "I'm A Bad, Bad Man", and "I'm an Indian Too"), but included "An Old-Fashioned Wedding". There were several major dance numbers added, including a ballroom scene. A sub-plot, which had been dropped from the 1966 revival, involving the romance between Winnie, the young sister of Frank Butler's assistant and Tommy, her part-Native-American boyfriend was also included, and Winnie is Dolly's sister rather than her daughter. In this version, the final shooting match between Annie and Frank ends in a tie. Read more on Last.fm. User-contributed text is available under the Creative Commons By-SA License; additional terms may apply.