His visit comes as Egypt's Coptic Christians reel from a series of jihadist suicide bombings in December and April that killed dozens of worshippers.
Francis is scheduled to visit the Cairo church bombed in December alongside Coptic Pope Tawadros II.
The 80-year-old pontiff landed in Cairo earlier on Friday before meeting President Abdel Fattah al-Sisi and then Al-Azhar's Grand Imam Ahmed al-Tayeb, one of the Muslim world's leading authorities.
Sisi, a former army chief criticised for rights abuses, welcomed Francis at his palace with a military brass band and priests lining up to greet the head of the world's 1.3 billion Catholics.
'Peace is holy'
Francis then headed to Tayeb's headquarters, sealing a recent improvement in relations between Catholicism and the Sunni branch of Islam.
Francis, who was shuttled from one engagement to another in a closed car on the first day of the tightly scheduled 27-hour visit, then gave a speech to a Muslim-Christian conference.
"Peace alone... is holy and no act of violence can be perpetrated in the name of God, for it would profane his name," Francis said.
The pope also took aim at what he called "demagogic forms of populism... on the rise," saying they were unhelpful to peace.
The pope was joined at the conference by Ecumenical Patriarch Bartholomew, Archbishop of Constantinople, the spiritual leader of the Orthodox world and a close ally.
In another speech with Sisi in the audience, Francis expressed support for Egypt's military campaign against ISIS group jihadists, who had bombed the churches and killed hundreds of troops.
But he also insisted on "unconditional respect for inalienable human rights such as equality among all citizens, religious freedom and freedom of expression."
Sisi has faced heavy criticism from rights groups for abuses since he led the military ouster of his Islamist predecessor Mohamed Morsi in 2013.
Before disembarking from his plane in Cairo, Francis had told reporters that his visit was a "journey of unity and fraternity. Less than two days but very intense."
His meeting with Tayeb, he said, would "be an example and a model for peace precisely because it will be a meeting of dialogue."
Security was extremely tight for the visit with Egypt under a state of emergency following the church bombings.
Police and soldiers stood guard outside the Vatican residence in Cairo on Friday and armoured cars were stationed outside the Coptic Orthodox Saint Mark's Cathedral, where Tawadros II's headquarters are located.
All of the country's churches have been placed under additional protection because of the risk of another assault timed to coincide with Francis being in the country.
Despite the dangers, Francis is expected to be taken to most of his engagements in a normal vehicle and electric golf carts.
"Please pray for my journey tomorrow as a pilgrim of peace to Egypt," Francis said on his Twitter account on the eve of his departure.
Before his visit, some roads had been festooned with posters showing Francis against the backdrop of the Pyramids, with a message that read: "Pope of peace in the Egypt of peace."
Visit to bombed church
John Paul II was the last pope to have visited Egypt in 2000, with his arrival also coming weeks after anti-Christian violence that killed about 20 Copts in January that year.
Vatican dialogue with the Muslim world, a priority for this pope, was set back significantly when Francis's predecessor Benedict XVI made a speech in 2006 in which he was seen as linking Islam to violence.
The now-retired German pontiff's 2011 comments condemning an attack on a Coptic church prompted Al-Azhar to denounce Benedict for meddling in Egypt's affairs.
One of the highlights of Francis's trip will be his visit on Friday to the church of Saint Peter and Saint Paul, which had been bombed by IS in December in attack that killed 29 people.
He will meet Pope Tawadros II first in his nearby headquarters before they lead a procession to the bombed church, which has since been renovated.
ISIS, which has threatened open war on the Christian minority, followed with twin church bombings in April that killed 45 people.
On Saturday, the pontiff will preside over a mass for the country's small Catholic community, estimated to number around 272,000 spread across various rites.
Egypt's Copts, who make up about 10 percent of the country's population of 92 million, are the Middle East's largest Christian minority and one of the oldest.
But they have suffered attacks throughout the years and many complain that they feel like second-class citizens.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)