His speech comes just weeks before British Prime Minister Theresa May is due to trigger Article 50 of the Lisbon Treaty, to begin the country's official divorce proceedings from the EU.
The former Luxembourg prime minister insisted that "as painful as Brexit will be, it will not stop the EU as it moves to the future."
Juncker laid out five "pathways to unity" for EU leaders to consider at a special summit in Rome on March 25 to mark the 60th anniversary of the bloc's founding treaty.
Another option would see Brussels pull back from many areas, including regional development, health, employment and social policy. Alternatively, the bloc could maintain the status quo, Juncker said, with limited progress on strengthening the euro single currency and limited defense cooperation.
The fifth option would involve a more federalist approach, "sharing more power, resources and decision-making across the board."
During his speech, Juncker hit out at "permanent Brussels bashing" by populist politicians all over the bloc, insisting that the EU was not responsible for each country's problems.
But he conceded that Brussels had often been put on a pedestal, and had failed to keep many of its ambitious promises, for example, addressing the bloc's high unemployment rate.
Looking to the future, Juncker said: "Our task will be to say clearly what Europe can and cannot do."
He called for EU states to respond to his suggestions by the end of the year, and decide on a course of action by the European Parliament elections in June 2019.
Note EU Digest: we support a strong and independent EU, as we have always done. But we have also voiced fo, and continue to do so, for more citizen involvement in the day to day running of EU, including to having the President of the Commission being elected by popular vote for a period of 5 years.
Read more: EU′s Juncker unveils post-Brexit vision for bloc | News | DW.COM | 01.03.2017