The America's highest civilian award was given by the president, saying the pontiff was "a light of faith, hope, and love that shines brightly across the world."
This marks the first time President Biden has awarded the Presidential Medal of Freedom with Distinction during his four-year term.
In a statement, the White House said the award is "presented to individuals who have made exemplary contributions to the prosperity, values, or security of the United States, world peace, or other significant societal, public or private endeavours".
Initially, President Biden had planned to present the medal to Pope Francis in person during his final overseas trip as president.
However, due to the California wildfires, the president cancelled his visit and instead bestowed the award upon the pontiff during a phone call.
They also discussed efforts to promote global peace and alleviate suffering.
The award, which can be presented with or without distinction. President Biden had previously presented the medal without distinction to several notable individuals, including Hillary Clinton, Bono, and Denzel Washington on January 5.
Mr Biden himself is a recipient of the award with distinction, recognised when he was vice president by then president Barack Obama in a surprise ceremony eight years ago.
