The trip to the mosque, the largest in Jordan, marked the second day of the pope's visit to the Middle East, the BBC reported.
Afterward, Benedict addressed local Muslim leaders. Earlier in the day he visited Mount Nebo, where the Bible says Moses saw the Promised Land before he died.
Vatican analysts said the pope is anxious to mend relations with Muslims and Jews on his eight-day sojourn to Israel and the West Bank, his first to the region as pontiff.
In remarks delivered at the King Hussein bin Talal Mosque, the pope urged Christians and Muslims to work toward peace.
Vatican spokesman Rev. Federico Lombardi said the 82-year-old pontiff did not remove his shoes or pray while in the mosque in Jordan, Britain's Telegraph reported.