On the final full day of the Pontiff's trip to the country huge crowds braved the heavy rain to see him at the capital Manila's biggest park.
Crowds cheered and applauded as the Holy Father arrived at Rizal Park in his popemobile wearing a plastic yellow rain poncho - the same one the faithful were given.
Francis spoke about the importance of young people during his homily: "We need to see each child as a gift to be welcomed, cherished and protected.
"This is the largest event in the history of the Pope"
Vatican spokesman
"And we need to care for our young people, not allowing them to be robbed of hope and condemned to a life on the streets."
The Vatican said it had been told by government officials the turn out was between six and seven million.
A spokesman said it was the biggest event "in the history of the Pope".
Earlier around 200,000 people came to Manila's Catholic university to see Francis who heard stories of the country's poverty ridden people.
Around a quarter of the Filipino population live below the poverty line.
The Pope was visibly moved when asked by an orphaned 12 year old girl why God had let her suffer so much.
"Why is God allowing something like this to happen, even to innocent children? And why are there so few who are helping us?" She said through tears.
Francis replied that he had no answer: "Only when we are able to cry are we able to come close to responding to your question.
"Those on the margins cry. Those who have fallen by the wayside cry. Those who are discarded cry," he said. "But those who are living a life that is more or less without need, we don't know how to cry."
"There are some realities that you can only see through eyes that have been cleansed by tears."
Hours before the mass started people had arrived to get a good spot in the park, with some camping outside.
Before the service Pope Francis met with the family of Kristel Padasas, a volunteer with Catholic Relief Services, who died at yesterday's mass in Tacloban when scaffolding fell on her.
Vatican spokesman Fr Federico Lombardi said her father was "consoled thinking that she had helped prepare the meeting of the people with the pope."
Up to 40,000 police officers have been deployed to protect the Pope.