Speaking in Munich, Kerry said that recent events had "overwhelmed" many Europeans, but that America is confident that Europe will emerge stronger.
"Here again however, I want to express the confidence of President Obama and all of us in America that, just as it has so many times before, Europe is going to emerge stronger than ever, provided it stays united and builds common responses to these challenges," he said.
"Now obviously, the US has a profound interest in your success as we do in very strong UK staying in a strong EU."
However, pro-Brexit Leave.EU hit out at Kerry's comments. "It might be convenient for John Kerry, who has repeatedly declined to support the UK in the Falklands, for us to be in the EU, but that doesn't mean it's good for us," said Leave.EU spokesman Jack Montgomery.
"Imagine if Kerry proposed a Pan-American Union in which an unelected Commission would control United States immigration policy, trade policy and regulations, among a host of other important matters. He would be run out of Washington DC on a rail."
Kerry's comments come ahead of an EU summit of leaders, where Prime Minister David Cameron is hoping to secure a deal on his reform agenda.
Cameron was in Germany yesterday, where he said the UK will never "retreat from the world", adding that it is in the EU's interests for the UK to stay in a reformed EU.