The meeting was keenly awaited as the two men have already clashed at a distance on issues including migration and climate change.
The 2016 United States presidential campaign saw the two men broadcast dueling messages to the world.
Meanwhile, Trump looked on as his wife and the pope laughed at the joke about his weight.
Trump and Francis certainly had differences to iron out during their meeting.
Their discussion was private, but after their meeting Francis handed him his book on the importance of protecting the environment and holding man largely responsible for climate change.
"Honor of a lifetime to meet His Holiness Pope Francis", a star-struck Trump wrote on Twitter before leaving Rome for Brussels and the next leg of his first overseas trip as USA president. The Pope, either at a loss for what to talk to Melania about or just morbidly curious, asked FLOTUS, "What do you give him to eat?". Bernie Sanders during the 2016 campaign as a fellow "radical" - has been at odds with Trump on capitalism, which Trump said in a 2015 interview he'd "scare" the pope into supporting. In February, Francis said that we should not be "focused on building walls". Donald Trump, who became the first U.S. president to visit the wall while in office, donned a yarmulke - a skullcap - which is customary; the site keeps stacks of them for visitors to wear. The pope said a year ago a man who thinks about building walls and not bridges is "not Christian".
Speaking with reporters aboard Air Force One, Secretary of State Rex Tillerson couldn't say whether climate change was discussed with the pope.More news: Congressman Al Green presses on with call for Trump impeachment despite threats
The first Jesuit pope said anyone who thinks of building walls instead of bridges "is not Christian", a comment that Trump called "disgraceful". "And that's a hard balancing act".
Trump later said via Twitter that it had been an "honor of a lifetime" to meet the pope. With other members of the president's retinue, they walked past seven Swiss Guards standing at attention in front of a white papal throne, halberds in hand. But she said there's also value in an American president engaging with the press on foreign soil. They were followed by other members of the president's 12-member delegation who included Secretary of State Rex Tillerson, H.R. McMaster, National Security Adviser, and Louis Bono, chargé d'affaires at the US embassy to the Holy See. The president then introduced his daughter, Ivanka, and the rest of his delegation, beginning with Mr. Kushner.
Trump told his host as he left, "Thank you". Trump responded: "Well I'll be reading them".
Francis then gave the president a small sculptured olive tree and told him through the interpreter that it symbolised peace.
The pope had presented Trump with a medallion engraved with an olive tree, the global symbol of peace.
The US President vowed to help Israelis and Palestinians achieve peace, as he ended the Middle East leg of his tour on Tuesday.
He said Trump "is not Christian".