Twelve-year-old Glyzelle Palomar wept as she asked the Pope: "Many children get involved in drugs and prostitution. Why does God allow these things to happen to us? The children are not guilty of anything."
Glyzelle was once homeless before being given shelter at a church-run community.
The visibly moved Pope responded: "She is the only one who has put forward a question for which there is no answer and she was not even able to express it in words but rather in tears."
Addressing a crowd of 30,000 people gathered at the University of Santo Tomas in Manila, the Pope was quoted by The Independent as saying: "I invite each one of you to ask yourselves, 'Have I learned how to weep, how to cry when I see a hungry child, a child on the street who uses drugs, a homeless child, an abandoned child, an abused child, a child that society uses as a slave?'"
Pope Francis later conducted a mass that set record attendance of an estimated six million catholic devotees with some people waiting overnight to get the best spot to see the pontiff.
Compassion for the poor was central to the Pope's visit in the Philippines, and he condemned "scandalous social inequalities" prevalent in the society.