Investigators say the shots were probably fired from a car caught on surveillance video in the Deer Valley High Parking lot, just before the shooting. Investigators say they've spoken to the car's owner and say he's cooperating. Police say the shooting may have been gang related.
The lockdown was lifted by late morning.
Deer Valley High School teachers tried to calm worried parents who nervously waited for the two-hour lockdown to come to an end.
"My daughter called me this morning about 8:50 screaming somebody got shot. I was like what?" said school parent Nakiesha Leslie.
The shooting happened at 8:30 on Wednesday morning on a side street just outside the school property line.
"At one point, our victim approached the vehicle and continued to have an exchange of words and then somewhere between three to five shots were fired," said Lieutenant Leonard Ormand from Antioch Police Department.
The 16-year-old was shot in the chest and arm and more shots were fired at another student with him. He ran and escaped being hit.
The victim was taken by helicopter to John Muir Medical Center in Walnut Creek and underwent surgery on Wednesday afternoon.
"All I do know is that the victim was conscious as he was placed into the helicopter and he was communicating with police just before that," said Deer Valley High School co-principal Scott Bergerhouse.
All 22 schools in the district were placed on lockdown following the shooting. Security at schools in neighboring Pittsburg was also increased as authorities continued their hunt for a suspect.
"Based on the description and age that we're getting, I would venture to say they're probably not high school students. I think if they were, we'd have information as to their identities," said Lt. Ormand.
The suspect's car is described as a tan, brown or gold compact sedan. It's an older model between five to 10 years old. It has tinted windows and oversized tires and rims.
Police say numerous people witnessed the shooting because of the busy time of morning it took place. They're asking anyone with information to call Antioch Police.