Francis and the American singer exchanged smiles when they embraced hands at the Unite to Care conference on Saturday.
Perry was also joined at the summit by her boyfriend, 41-year-old English actor Orlando Bloom.
In a post on Twitter, Perry said: "[I was] honoured to be in the presence of His Holiness's compassionate heart and inclusivity."
The meeting comes amid a lawsuit between the pop star and a group of nuns over the sale of a convent in the Los Felix area of Los Angeles, California.
Perry has sought to buy the eight-acre property and its Roman-villa style buildings for $14.5 million but the sisters have wanted to sell the property to a local businessperson.
Honored to be in the presence of His Holiness @Pontifex's compassionate heart and inclusivity. Thank you to @meditationbob and #TheCuraFoundation for making it all possible.❤️ #UniteToCure pic.twitter.com/EEPWJI2gkT
— KATY PERRY (@katyperry) April 29, 2018
Perry told followers on social media that she was invited to the event to speak about meditation - an activity used to help people relax, though it does not sit well with some Christians.
The 33-year-old has spoken in the past about her experience being raised by her committed Christian parents, Keith and Mary Hudson.
The fourth annual Unite to Cure conference explored how science, technology and modern medicine can impact societies - particularly poorer cultures.
The three-day meeting is organised by the Vatican's Pontifical Council for Culture and the New York-based Curia Foundation.
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