"It would seem that they (the extremists) do not want there to be any Christians, but you bear witness to Christ," he said in a video address timed to coincide with a visit Saturday by French Cardinal Philippe Barbarin to the Iraqi Kurdish city of Arbil.
"I think of the wounds, of the pain of women with their children, the elderly and the displaced, the wounds of those who are victims of every type of violence," Francis said according to a transcript.
Thousands of Christians took refuge in Arbil after IS jihadists in June overran Mosul, Iraq's second city, and forced hundreds of thousands of them, as well as members of the Yazidi community, to flee their homes.
"Due to an extremist and fundamentalist group, entire communities, especially, but not only, Christians and Yazidi, have suffered and continue to suffer, inhuman violence because of their religious and ethnic identity," the pope said.
"Christians and Yazidi have been forced out of their homes; they have had to abandon everything to save their lives, but they have not denied their faith."
"Even holy buildings, monuments, religious symbols and cultural heritage have been affected by the violence, almost as if to cancel every trace, every memory of the other."
Last weekend, the pontiff visited Turkey where he met Bartholomew I, the ecumenical patriarch and spiritual leader of the world's roughly 250 million Orthodox Christians.
The two clerics issued a joint statement in which they spoke out against anti-Christian violence in the region.
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After his visit, the pope urged Muslim leaders worldwide to "clearly" condemn terrorism carried out in the name of Islam, and called for an end to the persecution of Christians in the Middle East.
Francis said he had told Turkish President Recep Tayyip Erdogan that "it would be wonderful if all the Muslim leaders of the world -- political, religious and academic, spoke up clearly and condemned" violence which damages Islam.
In his address Saturday, Francis told the Christians in Arbil: "I too would like to be there with you, but since I am unable to travel, I will do this instead," referring to the video message.
On Thursday, Al-Azhar, Sunni Islam's most prestigious centre of learning, urged Christians in the Arab world to "stay rooted in their homelands" in the face of jihadist violence and not flee into exile.
"We condemn the forced exile of Christians and other religious or ethnic groups," it said.
Barbarin is the Roman Catholic archbishop of Lyon and his diocese is twinned with that of Mosul. He is on his second trip to Arbil since Mosul fell, having visited in July.
Before leaving France, Barbarin said his trip was to "point to the destiny of those who have remained faithful to Christ and who could be forgotten in the twists and turns of history."
In Arbil, he celebrated mass to mark the upcoming Catholic feast of the Immaculate Conception, after which there was a candlelight procession with 5,000 candles he had brought from France.
Marteen Offi is a refugee from Qaraqosh, which was once Iraq's largest Christian town.
"We are a bit sad because we always held this procession with the candles at Christmas in Qaraqosh," he said.
"But at the same time, all these people praying, despite everything that has happened. They have the heart to do something and not just stand idly by," said the 23-year-old, who works with an association that cares for young displaced children.