McIntyre will replace the departing Norbert Leo Butz, who leaves his role July 18 to be part of the Old Globe Theatre's production of Dirty Rotten Scoundrels.
McIntyre was previously mentioned as being in talks for the part.
A Tony nominee for her work in Urinetown, Thompson will replace Tony Award winner Kristin Chenoweth. Chenoweth ends her Wicked run July 18 when her contract ends and will begin filming the movie version of the classic TV series "Bewitched."
Due to join the cast one month earlier, on June 20, will be Randy Harrison, star of Showtime's hit series "Queer As Folk." He will make his Broadway debut as Boq, staying with the show only until July 25.
Christopher Fitzgerald, who originated the role of Boq, heads to the Williamstown Theatre Festival next month. McIntyre has appeared Off-Broadway in tick, tick . . . BOOM! and in the Los Angeles Reprise! mounting of Babes in Arms. He was also seen in the film version of Jones and Schmidt's The Fantasticks.
Harrison, who received his BFA in theatre from the University of Cincinnati College Conservatory of Music, made his Off-Broadway debut in the MCC production of A Letter from Ethel Kennedy and also starred in the International Fringe Festival production of Deviant. His other theatrical credits include Shopping and Fucking, Violet, Hello Again, Children of Eden and 1776. Harrison can currently be seen as Justin, the young gay artist, on Showtime's "Queer as Folk" series.
Jennifer Laura Thompson received a 2002 Tony Award nomination for her performance as Hope Cladwell in Urinetown. She also appeared on Broadway as Ariel Moore in the original cast of Footloose as well as in the City Center Encores! production of Strike Up the Band. Off-Broadway Thompson was seen in Tip-Toes, Little Fish and A Doll's Life.
The Stephen Schwartz-Winnie Holzman musical won three Tony Awards, including a Best Leading Actress in a Musical prize for co-star Idina Menzel.
With a score by Stephen Schwartz, a book by Winnie Holzman and direction by Joe Mantello, Wicked features choreography by Wayne Cilento and plays the Gershwin Theatre, 222 West 51st Street. Tickets are available by calling (212) 307-4100 or by visiting www.ticketmaster.com.