Aquino died Saturday of colon cancer at age 76.
The mourners lined up amid rain and wind for a public viewing of Aquino's body, with many remembering her as a leader who restored democracy to the Philippines, GMANews reported.
"The family is very thankful. They didn't expect this," Deedee Sityangco, a family friend and former Aquino spokesperson said.
An estimated 300 police officers were stationed around the school where a memorial mass was conducted Sunday and another 200 officers were stationed inside, Joey Mendoza, a memorial organizer said.
The scene inside was emotional, especially toward the end of the service when the protest song "Bayan Ko" was sung and many raised clenched fists in honor of Aquino and her husband, Benigno Aquino, Jr., an opposition leader who was assassinated in 1983, witnesses said.
Aquino will be buried Wednesday at the Manila Memorial Park next to her husband, the Philippine Daily Inquirer said.