The actress rep confirmed to Us Weekly that the couple is expecting a child, their second.
Rumors of a possible pregnancy slowly circulated last week after Emily was photographed wearing an oversized coat in New York while shooting the film "The Girl on the Train."
John, meanwhile, has been at the Sundance Film Festival in Park City, Utah promoting his newest movie "13 Hours: The Secret Soldiers of Benghazi."
Emily and John have been married since 2010 when they tied the knot in Italy. The have one child, daughter Hazel, who was born in February 2014.
John is relatively open about this family life. Last month he swooned over his daughter.
"She is talking. She is talking a lot. She is starting to do little bits. It's hilarious," he told Ellen DeGeneres. "[Instead of saying] 'Where's Daddy?' she asks, 'Where is that Daddy?'"
The little tyke even has a British accent at times, much like her mom.
"She says, 'Wuter,'" he said, laughing. "Just wait till she gets to kindergarten when people go, 'What's that accent?' And she'll go, 'Water! Water!'"
Emily can't help but gush about their daughter, too, telling People magazine that motherhood is "heaven."
"It is that and more," she said. "I know that everybody says that. Everybody says, 'Oh it's the best -- it's the best thing ever!'"
She continued, "You don't know what to expect because it's just completely, existentially out of anything that you've ever experienced before, and it's quite indescribable."