"The newly elected president is delighted to see Britain leave" the European Union, Juncker told a congress of the European People's Party (EPP) in Malta on the day after one of the bloc's biggest members started the exit process.
"If he carries on, I am going to promote the independence of Ohio and Austin, Texas,'" he said in German to chuckles from delegates in Valletta.
Juncker, who was in Malta with EU President Donald Tusk, German Chancellor Angela Merkel and Spanish Prime Minister Mariano Rajoy, urged the remaining 27 EU nations to pull together.
"Brexit is not the end of everything, but we must make it a beginning of something that will be new, stronger and better."
Britons last year voted 52 percent to 48 percent in favor of Brexit, leaving the country bitterly divided.
Trump said the vote to leave the EU was a good idea and that other countries would likely follow suit.
In an interview last week, Juncker said he had asked Trump's administration not to encourage other countries to ditch the bloc.
