The Argentinian pontiff's first point of call was a set of colourful pre-fabricated buildings serving as a makeshift school.
Amatrice's school was destroyed in the quake despite having been expensively renovated to make it quake resistant a few years ago.
In keeping with his desire to make a relatively low-key visit to an area where nearly 300 people died, the 79-year-old pontiff's trip to the shattered town of Amatrice and the devastated nearby hamlets of Accumoli and Arquata del Tronto was only announced to the media after he had arrived.
In a poignant image tweeted by the Vatican press office, Francis stood briefly in silent prayer in the closed-off "red zone" of Amatrice, his stooped silhouette framed by the shells of condemned buildings and piles of rubble.
He later repeated the gesture outside the ruins of the St Francesco church in Accumoli, having spent two hours over lunch chatting with 60 pensioners in a retirement home where some of the elderly victims of the quake are now housed.
"I did not come earlier so as not to create any problems, knowing the state you were in," he told survivors. "I did not want to cause any bother."
"But from the outset I felt I had to come to you, simply to tell you that I am with you, nothing more, and that I am praying for you."
After blessing the crowd in Amatrice and saying a brief Ave Maria prayer, Francis issued a message of hope for an area still struggling to come to terms with the scale of Italy's deadliest quake since the 2009 L'Aquila disaster.
Vatican spokesman Greg Burke tweeted pictures of the pope greeting youngsters and shaking hands with a visibly-moved middle-aged man. The man lost his wife and two children in the disaster, according to the Vatican spokesman.
"There are many dear ones who have left us, who fell here under the masonry. We pray to the Madonna for them, we all do together. "Always look forward. Go forward, have courage and help each other. We walk better together, on our own, we cannot get there."
Francis had confirmed his intention to visit the quake-hit area on his flight home from Georgia and Azerbaijan on Sunday, but had not divulged when he intended to go.
He said he wanted to make his visit "privately, alone, as a priest, a bishop, a pope. But alone," in order to be "near the people."
The government has estimated the cost of the damage done to the area hit by the quake at four billion euros ($4.5 billion) and has vowed to rebuild the worst-affected communities where they were, having ruled out any relocations.
Amatrice worst hit
Around 1,800 people remain housed in temporary accommodation - either tented villages or hotels in the surrounding area, according to the latest update issued last week.
Francis's statement on Sunday was a reaffirmation of a pledge he made to worshippers on August 28th, four days after the disaster, to visit the area hit by the 6.0 to 6.2 magnitude quake.
"As soon as possible, I hope to come and see you, to bring you the comfort of faith, the tenderness of a father and a brother," he said in St Peter's Square in the Vatican City.
The earthquake, which was felt in Rome, 150 kilometres (93 miles) from the epicentre near Amatrice, killed 297 people and injured hundreds more.
Around two thirds of the deaths occurred in Amatrice, a beauty spot and popular tourist destination which was packed with holiday-makers when the quake struck at the height of the summer season.
The quake struck an area only 50 kilometres from the city of L'Aquila, which was hit by a 2009 earthquake in which more than 300 people perished.