Around 50,000 police and soldiers are on the streets, in what is the country's biggest security operation to date.
In 1970, a Bolivian artist tried to stab Pope Paul VI as he arrived at Manila airport.
Financial markets in the capital Manila have also closed, and the government's declared a three-day public holiday to clear traffic there.
The pontiff is meeting survivors of Typhoon Haiyan, which killed more than 6,000 people last year, in the central province of Leyte.
Pope Francis will also be delivering an open air Mass at Tacloban City airport, which is also in Leyte and expected to draw two million people.
He's also delivering an open air Mass in Manila's largest park, where six million people are expected to attend.
The Philippines President, Benigno Aquino, has personally inspected the routes for Pope Francis' motorcade. Concrete barriers with wire meshing have been used to hold back the crowds.
President Aquino urged Filipinos to follow safety and security rules in a television address, after two people were killed in a stampede during a religious procession on Friday.
Approximately 4 in 5 Filipinos are Catholics, amounting to around 80 million people.
Watch Pope Francis arriving in the Philippines:
