The March 25 summit will mark the 60th anniversary of the bloc's founding treaty. The pontiff will meet the leaders in the afternoon, the sources said.
The pope has already received EU leaders at the Vatican in May 2016 when he was presented with the bloc's Charlemagne Prize for his contribution to European unification.
In a speech at that ceremony he called on them to "tear down the walls" and build a fairer society.
The pope also made a speech to the European Parliament in Strasbourg in November 2014.