War of the Worlds star Cruise, 43, and Holmes, 27, got engaged in June after a two-month whirlwind romance.
Cruise’s publicist, his sister Lee Anne DeVette, said: “Katie is pregnant. They are expecting a baby.”
She declined to give details of the due date but said Batman Begins actress Holmes had “never felt better”.
“They are very excited,” added Ms DeVette.
The couple have yet to announce their wedding date.
Cruise, who has been married twice before, has two other children – Connor, 10, and Isabella, 12, whom he adopted with previous wife Australian Oscar-winner Nicole Kidman.
They split in 2001 after 10 years of marriage.
Cruise and Holmes first revealed they were dating in April and announced their engagement at a press conference in Paris two months later.
Cruise had previously been protective about his private life but he expressed his love for Holmes, a star of US TV teen drama Dawson’s Creek, in interviews and in a series of public displays of affection.
During an appearance on Oprah Winfrey’s US TV show in May, Cruise repeatedly jumped up and down on the talk show host’s sofa and yelled: “I’m in love! I’m in love.”
Actor Jamie Foxx and director Steven Spielberg were among the Hollywood figures to stand up for Cruise amid media scrutiny of his behaviour.
Spielberg said Cruise was “punished” by the media for showing his affection for his fiancee in public.
Cruise also spoke out about his membership of the Church of Scientology.
Before he began dating Holmes earlier, Cruise went out with Spanish actress Penelope Cruz for three years until the relationship ended in January.
The star of films such as Jerry Maguire and The Last Samurai was married to actress Mimi Rogers before Kidman.