Francisco and Jacinta Marto, aged nine and seven at the time of the apparitions, died two years later of influenza, leaving their cousin Lucia dos Santos to share the secret messages with the world.
The pontiff held a mass in the shrine town Saturday to canonize the Marto siblings, making them the youngest saints who did not die as martyrs in the history of the Catholic Church.
Hundreds of thousands of pilgrims attended the celebrations as church groups, families and individuals flocked to Fatima, 90 miles north of Lisbon.
Dos Santos, who was nine when she experienced the visions, grew up to become a Carmelite nun and lived until the age of 95.
She later revealed the prophecies in a memoir and a letter to the Vatican. She is currently on track for beatification, the first step towards becoming a saint. However, the process could not begin until after her death.
Pope Francis’ trips abroad often have geopolitical or ecumenical undertones. But his visit to Fatima is purely religious.
“This is a special trip,” Pope Francis told journalists on board the flight to Portugal. “It is a voyage of prayer.”
While the prophecies refer to events of the twentieth century, the Pope drew parallels between the Virgin Mary’s century-old call for penance and reconciliation during World War I and today.
At a candle light vigil Friday, the pope told faithful to “tear down all walls and spread peace and justice.”
Pope Francis has become the fourth Pope to visit Fatima, after Paul VI, John Paul II and Benedict XVI, and will join millions of pilgrims who visit the site every year.
Portugal has boosted security ahead of the pontiff’s visit and has reinstated border controls restricting freedom of movement from other European states.