The service for Christina Taylor Green, 9, at St. Elizabeth Ann Seton Catholic Church was private, the Los Angeles Times reported. But hundreds were drawn to the church, standing on the roadside as the hearse carrying her body drove by.
The funeral was the first for victims of the shooting.
The largest flag to survive the destruction of the World Trade Center on Sept. 11, 2001, was suspended over the entrance to the church, The Washington Post said. Christina was born that day.
Tucson Bishop Gerald Kicanas celebrated a Mass of Resurrection, the Times said.
Christina, recently elected to the student council at her middle school, went to Rep. Gabrielle Giffords' appearance at a Tucson shopping center with an adult friend because she wanted to meet a woman active in politics.
Six people were killed and 13 wounded in the shooting, allegedly carried out by Jared Lee Loughner, 22. Giffords, D-Ariz., believed to be Loughner's intended target, remained in critical condition Thursday. She was shot in the head.
Both neighbors and strangers rallied to support Christina's family. She was to be laid to rest in a handmade coffin donated by a community of Trappist monks in Iowa while a house across the street from the church displayed a sign: "Your community is standing with you."
Jimmy Sands, a New York City firefighter, brought the 50-pound flag to Tucson, The Arizona Republic reported.
The family is "delighted" the flag will be displayed at the service, St. Elizabeth Ann Seton parish administrator Theresa Bier told the newspaper.
U.S. President Barack Obama praised Green at a University of Arizona memorial service Wednesday night and said he wanted Americans "to live up to her expectations."
"I want our democracy to be as good as she imagined it," he said.