The pair met after an earthquake in central Italy killed more than 250 people.
Facebook has been a part of disaster responses across the world, allowing people to register when they're safe.
Mark Zuckerberg also presented Pope Francis with a small solar-powered aircraft called Aquila (below), which can be used to provide internet to remote regions.
The Facebook founder later said on his own social media platform: "You can feel the Pope's warmth and kindness, and how deeply he cares about helping people.
"We told him how much we admire his message of mercy and tenderness, and how he's found new ways to communicate with people of every faith around the world.
'We also discussed the importance of connecting people, especially in parts of the world without internet access."
The Vatican said in a statement: "Together they spoke about how to use communications technology to alleviate poverty, encourage a culture of encounter, and to communicate a message of hope, especially to the most disadvantaged."
Mr Zuckerberg also met the Italian Prime Minister Matteo Renzi (below), where they discussed the recent Italian earthquake as well as Facebook's investment into the Italian economy.
