Reports suggest that the two met for almost an hour, which is longer than had previously been expected.
A statement released by the White House ahead of the trip said "The President looks forward to discussing with Pope Francis their shared commitment to fighting poverty and growing inequality".
The President has previously described the Pope as "a man who lived the Christian Gospel" and has apparently been inspired by the Pontiff's heart for justice and equality. Upon greeting Pope Francis he expressed his pleasure at their meeting, saying he is "a great admirer" of the Catholic leader.
The two publically exchanged gifts before their private meeting. Obama bought a custom made seed chest made with wood from the first cathedral to be built in the US, while Pope Francis presented the President with a plaque and a copy of his first apostolic exhortation entitled Evangelli Gaudium, the Joy of the Gospel.
The Vatican described the meeting today as "cordial" and said they had exchanged views on current international themes.
"Hope was expressed that, in areas of conflict, there would be respect for humanitarian and international law and a negotiated solution between the parties involved," the Vatican said.
"In the context of bilateral relations and cooperation between Church and State, the parties discussed questions of particular relevance for the Church, such as the exercise of the rights to religious freedom, life and conscientious objection, as well as the issue of immigration reform.
"Finally, the parties stated their common commitment to the eradication of human trafficking throughout the world."