Merkel and Francis met for about 40 minutes in the Apostolic Palace on Saturday, focusing on the Group of 20 summit that Germany is hosting in Hamburg on July 7-8.
The Vatican said the talks focused on the need for the international community to combat poverty, hunger, terrorism and climate change.
Merkel told reporters she briefed the pope on Germany's G-20 agenda, which she said "assumes that we are a world in which we want to work together multilaterally, a world in which we don't want to build walls but bring down walls".
Francis has consistently called for nations to build bridges not walls - including in reference to the border wall the Trump administration wants to build with Mexico.
Merkel said Francis encouraged her to fight for international agreements, including the 2015 Paris climate accord, which aimed to curb heat-trapping emissions.
"We know that regrettably, the United States is leaving this accord," Merkel said.
As he did when President Donald Trump visited last month, Francis gave Merkel a copy of his environmental encyclical, "Praise Be," which casts fighting climate change and caring for the environment as an urgent moral obligation.