The security operation which runs through Sunday is deploying some 6,000 members of security and emergency services.
The head of Roman Catholic Church will arrive on Friday at the site where 100 years ago apparitions of the Virgin Mary were reported by two child shepherds who the pope will canonise as saints.
Pilgrims began arriving Thursday for the event, going through security controls at various access points to the giant esplanade facing the Sanctuary of Our Lady of Fatima.
The security operation which runs through Sunday is deploying some 6,000 members of security and emergency services, the government said, while adding the security alert level remains at "moderate".
While Portugal has not been a target in the wave of attacks by extremists in Europe, the country has special reason for concern over the pontiff.
On May 12, 1982, there was an attempted attack on then pope John Paul II on his pilgrimage to Fatima by a fundamentalist Spanish priest armed with a bayonet.
Border controls have been reinstated in the EU country through the weekend and airspace over the area is closed. Measures for jamming electronic signals have been established to prevent any flights of drones.
Other popes have been drawn to the Fatima shrine, including Benedict XVI in 2010 who was met there by half a million people.
More than a million pilgrims are expected to come see Pope Francis and to mark the centenary of the apparitions in a country that is 89 percent Catholic.
The Virgin is said to have appeared six times in Fatima, north of Lisbon, between May and October 1917 to three impoverished, barely-literate children -- Jacinta, 7, Francisco, 9, and their cousin Lucia, 10.
She apparently shared three major prophesies with the trio at a time marked by the ravages of the First World War and Church persecution in a relatively new Portuguese republic.
On Saturday -- the 100th anniversary of the Virgin Mary's first reported apparition -- Pope Francis will canonise Jacinta and Francisco who were apparently responsible for two miracles.