The 83-year-old US-based media mogul flew in to hold discussions with staff after the trial of former News of the World journalists concluded with Brooks being acquitted but a former editor of the tabloid, Andy Coulson, being convicted of hacking.
News UK is the parent company of The Sun, The Times, The Sunday Times and the now-defunct News of the World.
Murdoch was photographed being driven away from a property in Mayfair in central London today, reading a copy of The Sun, and then went to the offices in Wapping, east London.
Brooks, who was Murdoch's trusted lieutenant in Britain, was expected to make a public statement later today.
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Murdoch had strongly supported Brooks following her arrest in 2011, shortly after he shut down the News of the World when it emerged the paper had hacked into the voicemail of murdered schoolgirl Milly Dowler.
Brooks, 46, rose from humble beginnings to become editor of the News of the World and The Sun, which is read by millions.
She had close links to politicians including Prime Minister David Cameron and his predecessor Gordon Brown.
The prime minister apologised to parliament yesterday, saying it had been the "wrong decision" to take on Coulson in 2007.
But Cameron denied he had ignored warnings about Coulson's activities at the tabloid, which hacked the phones of celebrities including actors Jude Law and Sienna Miller, politicians and crime victims.