"(The pope) does everything possible to achieve peace and harmony throughout the world," Zelenskiy said in a tweet after their meeting at the Vatican.
"I asked for help with the release of Ukrainians captured in Donbass, Crimea and Russia," he said.
Relations between Ukraine and Russia collapsed following Moscow's annexation of the Crimean peninsula in 2014 and its subsequent support for separatists in a conflict in eastern Ukraine.
The Vatican has diplomatic relations with both Ukraine and Russia.
Ukrainian government forces and pro-Russian separatists in the east completed a large-scale prisoner swap on December 29 in the breakaway Donbass region. It is not clear how many Ukrainian government soldiers are still being held, but activists say there are about 100.