Ye Meng Yuan, 16, a Chinese student, died of multiple injuries from being run over by what officials believe was a special firetruck used to spread fire-suppressing foam.
San Francisco Fire Chief Joanne Hayes-White apologized to Yuan's family and said she was trying to arrange a meeting with them.
"It's very difficult and devastating news for all of us," Hayes-White said.
The family was upset after learning the details of the girl's death and wants the girl's body returned to China, San Mateo County Coroner Robert Foucrault said.
"It was a difficult conversation," he said.
It was unclear how the teenager got from the airplane to the spot where she was killed. Investigators believe she was down on the ground and not standing up during the "volatile" and "dangerous" aftermath of the plane crash, Hayes-White said.
The circumstances are being investigated by San Francisco police and the National Transportation Safety Board.
Foucrault declined to go into detail on how he determined the teenager was alive before she was struck, but said there was internal hemorrhaging that indicated her heart was still pumping at the time.
Authorities confirmed last week that Yuan was hit by a vehicle racing to extinguish flames that broke out on the Boeing 777 during the July 6 crash.
Police said she was on the ground and covered in fire-retardant foam that rescuers had sprayed on the wreckage.
Yuan and her middle school classmate, 16-year-old Wang Linjia, died at San Francisco International Airport. The other victim, 15-year-old Liu Yipeng, died at a hospital July 12. Dozens of others were injured, though most not seriously.
Yuan and Linjia were students at Jiangshan Middle School in Zhejiang, an affluent coastal province in eastern China, Chinese state media has reported.
They were part of a group of students and teachers from the school who were heading to summer camp in Southern California. Yuan and Linjia were seated at the back of the plane, federal investigators have said.
Meanwhile, the probe into the crash itself continues. Investigators have said the plane came in too low and too slow, clipping its landing gear and then its tail on a rocky seawall just short of the runway.