The young victim has only been identified as a 9-year-old girl from Bakersfield.
Authorities say she first got sick on Saturday but she was perfectly fine the last day she went to school. However, she did not receive her flu shot.
Public Health Officer Claudia Jonah said, "Flu is not something to take lightly. It's always something to do everything that's available to you to protect yourself and other."
Health officials say the school she attended is being thoroughly disinfected following her death. A letter was sent home to parents in the school district to notify them about what happened.
Grief counseling is being made available to students on Monday.