The European Commission president said he hopes "the day will come when the British re-enter the boat".
Speaking at a press conference in Brussels after a meeting of the 27 other EU leaders, Mr Juncker said: "I don't like Brexit because I would like to be in the same boat as the British.
"The day will come when the British will re-enter the boat, I hope.
"But Brexit is not the end of the European Union, nor the end of all our developments, nor the end of our continental ambitions."
Theresa May was not present for the talks in Brussels, with the leaders of the other 27 nations considering the future of the bloc after Brexit.
With the Prime Minister expected to trigger Article 50 within days, the meeting was the last chance for the leaders to gather together before the formal Brexit process begins.
German Chancellor Angela Merkel confirmed that if Mrs May invokes Article 50 next week, there would be an extraordinary meeting of the EU 27 on April 6.
If Article 50 is triggered later this month, the meeting would be pushed back to later in April.
"We are well-prepared and we shall wait with interest, but which day in March it will be is not of such prime importance," she said.
Brexit had been a "wake-up call" to the other EU members to prepare for the future, she said at a press conference.
European Council president Donald Tusk said the EU would be ready to respond within two days of Mrs May triggering Brexit, amid speculation that she could invoke Article 50 on Tuesday if the Brexit Bill clears Parliament on Monday, when MPs are expected to overturn Lords amendments.
Further time has been allocated later in the week for a possible session of "parliamentary ping-pong" if peers insist on reinstating their amendments, but if they do not Mrs May could have the legal authority to fire the Brexit starting gun on Tuesday, when she makes a Commons statement on the Brussels summit.