The couple's daughter, Hazel, will turn two on February 16 and she will be joined by a little brother or sister this summer, a representative confirms to Us Weekly.
The Devil Wears Prada star wed fellow actor John, 36, in Italy in 2010 after two years of dating.
Emily, 32, has yet to display her growing baby bump in public, but she was photographed bundled up in a big coat on the streets on New York City last week, while filming the movie adaptation of The Girl on the Train, based on the bestselling novel of the same name by Paula Hawkins.
The news of the actress' pregnancy emerges days after her ex, Canadian singer Michael Buble, became a father for the second time. His wife, Luisana Lopilato, gave birth to a son named Elias on Friday.
The singer tied the knot with the 28-year-old Argentinian model and actress in 2011 and welcomed their first child, Noah, in 2013.
Michael and Emily dated for three years until 2008, when they split amid rumors of the crooner's infidelity.
The Haven't Met You Yet star previously confessed he had been "a jerk" for cheating on Emily, who dumped him after photos of the 40-year-old in another woman's bed surfaced.
Despite Michael's candor, Emily vowed to never discuss the reasons for their love split during a more recent chat with U.S. DJ Howard Stern in September last year.
"I never want to talk about it," she said. "I can't do it."
However, Emily did open up about her happy times with the singer, revealing the stars "had a good time" during their courtship, and although she is no longer in touch with the Canadian's family, she is still very fond of them: "I love his family. I still do," she admitted.