Kerry, who flies to Brussels and London on Monday for crisis talks with EU and British leaders, said the ideal of unity must remain paramount as Britain negotiates "Brexit".
"An EU united and strong is our preference for a partner to be able to work on the important issues that face us today," Kerry told reporters during a visit to Rome.
"One country has made a decision, obviously it's a decision that the United States had hoped would go the other way," he said, alongside Italian Foreign Minister Paolo Gentiloni.
Gentiloni said Brexit demonstrated the need for the EU to change.
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"We are working to relaunch the Union in light of the decision by the British electorate.
"Our historic friendship with Britain and our alliance through NATO are not up for discussion.
"The challenge we have before us is to translate a crisis into an opportunity by turning a difficult moment into the occasion to relaunch the EU."
But Kerry said he had no doubt that Europe would pull together and reassure the markets, noting that even without Britain the EU single market counts 455 million consumers.
President Barack Obama had also made clear his concern about the referendum, and now US officials are scrambling to try to stop the political crisis harming Western unity.
Kerry arrived in Rome today on a planned visit to have lunch with Gentiloni and a working dinner with Israeli Prime Minister Benjamin Netanyahu.
Mogherini had been expected to meet Kerry in Rome today, but she was busy dealing with the fallout of the dramatic vote, which stunned European and world leaders.
From Brussels, Kerry will continue to London to see Foreign Secretary Philip Hammond and other officials from outgoing British Prime Minister David Cameron's government.
Hammond and Kerry are expected to hold a joint news conference before Kerry leaves to return to Washington.
Obama and Kerry have been at pains to insist the vaunted "special relationship" between Washington and London will survive what US officials view as the Brexit debacle.