The website Deadline broke the news on Thursday, adding early indications are the divorce will not impact the 82-year-old’s media holdings.
The New York Times confirmed the report, with Amy Chozick tweeting: “Rupert has filed for divorce. Wendi has been informed.”
Rupert Murdoch divorce filing says the "relationship between husband and wife has broken down irretrievably.”— Amy Chozick (@amychozick) June 13, 2013
Deng has been famously protective of her husband – most notably when she defended him from an attack with a pie made of shaving foam.
Murdoch had been giving evidence to the Commons Culture, Media and Sport Committee about the phone-hacking scandal in 2011 when Jonathan May-Bowles - aka Jonnie Marbles - launched the pie at the him.
Deng leapt to her feet and slapped May-Bowles on the head. He was sentenced to six weeks in jail after admitting assault and causing harassment, alarm or distress.
Comedian David Baddiel has already referenced the attack on Twitter:
Ah! How quickly a newspaper magnate forgets being protected from custard pie attacks...— David Baddiel (@Baddiel) June 13, 2013
Deng and Murdoch met in Hong Kong in 1997 and married in 1999, less than a month after his divorce from former wife Anna Maria Torv Murdoch Mann was finalised.
The couple have two daughters, Chloe and Grace.