The president gave the Pope a tiled scene of old Jerusalem.
After the meet and greet, both heads of state discussed, privately, the troubled situation in the Middle East.
The Vatican says the discussion focused specifically on the need to find a just and lasting solution to the long standing Israel-Palestinian conflict.
The Presidents visit comes after days of protests in the West Bank and Gaza.
Protestors criticized the presidents decision to delay sending a report to the U.N General Assembly, the report accused Israel and Hamas of war crimes.
The conflict between Israel and Palestine has lasted more than six decades.
After his visit to the Holy Land in May, the Pope urged cooperation and mutual respect between all sides and said he believes a two state solution could be a reality.