Trump, who exchanged sharp words with the Pope during the US election campaign last year, received a tribute from the Swiss Guard in a Vatican courtyard when he arrived, reports Reuters.
There was no small talk with the press beforehand, and the two talked privately for about 30 minutes with translators.
The men looked more relaxed after the meeting, with the Pope smiling and joking with Trump and his wife Melania.
Francis gave Trump a tiny olive tree and told him it symbolised peace.
“It is my desire that you become an olive tree to construct peace,” the Pope said in Spanish.
Trump responded: “We can use peace.”
As the US delegation left, Trump told the Pope he won’t forget his words.
The Vatican said the meeting was “cordial” and it hoped there could be “serene collaboration” between the US government and the American Catholic Church, including “assistance to immigrants”.
The US Catholic Church hierarchy opposes Trump’s attempt to cut federal assistance for cities that give sanctuary to illegal immigrants.
It also opposes his plan to build a wall on the US border with Mexico.
The Pope said last year a man who thinks about building walls and not bridges is “not Christian”.
Trump responded that it was “disgraceful” of the Pope, who represents just over half of the world’s two billion Christians, to question his faith.