It came as a June 30 deadline looms for a deal that, which Israel has long opposed, causing friction with the White House.
Brennan met his counterpart Mossad chief Tamir Pardo and other intelligence officials, as well as Prime Minister Benjamin Netanyahu, Haaretz reported, citing "senior Israeli officials."
They discussed the emerging Iran deal and Tehran's Influence around the Middle East.
Netanyahu's staunch opposition to any agreement with Iran has helped bring his relations with US President Barack Obama to an all-time low.
In March, the Israeli premier controversially took his campaign to the US Congress, calling on lawmakers to block any deal between the powers and the Iran.
The Iran issue was also set to be high on the agenda of a separate visit to Israel by the chairman of the US Joint Chiefs of Staff, General Martin Dempsey.
Dempsey, who arrived on Monday, is due to hold talks with War Minister Moshe Yaalon and armed forces chief of staff Lieutenant General Gadi Eizenkot, AFP reports.