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."
He added that the prospect of the UK leaving the EU was strengthening the resolve of other member states, The Independent reported.
"The Brexit issue is encouraging the others to continue, unfortunately without the British," he said.
It comes after the European Parliament's chief Brexit negotiator said EU citizens in Britain were the victims of “political games” and that their rights must be the first item in exit talks.
Guy Verhofstadt called for the fate of those three million EU nationals, and of British ex-pats, to be settled before negotiations on the rumored £50bn ‘divorce bill’ – long thought to be the key early dispute.
Mr. Verhofstadt said the Parliament would agree a resolution soon after the Article 50 exit clause was triggered in the next few weeks, which it would expect to guide those talks.