"Removing young people from their families is not going to have a positive effect on either the youngsters or their families," the pontiff said during a press conference on the return leg of a five-day Colombia trip.
Francis said he knew of Trump's decision last week to abrogate an order issued by his predecessor Barack Obama that protected around 800,000 young people by granting them temporary legal status.
"I don't know how the decision was taken," he said, adding: "I hope he will reconsider".
Trudeau and the Pope's meeting brings out another viral picture
The move gives the so-called "Dreamers" -- many of them Hispanic who are now in their twenties -- somewhere between six and 24 months before they become illegal and subject to potential deportation.
"I have heard the US president present himself as a pro-life man, and if he is that he will understand the importance of the family, and life, and how the family unit must be defended," Francis said.
Trump's move fulfilled a campaign promise of zero tolerance toward illegal immigrants.
But the president insisted he was showing compassion for the Dreamers, many of whom know only the United States and speak only English, by giving Congress six months to craft a lasting legal solution.
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