None of the victims' ages have been released.
Before they were evacuated, terrified students took to Twitter to share frightening pictures of their classmates hiding on the floor.
"At freeman elementary currently. I am a junior, evacuated from the high school. At least 4 shot," one student wrote.
Sheriff's deputies went "floor to floor", "room to room" to search the school building to account for all of its students.
At around 11.30am, Fire Department Chief Brian Schaeffer said there was no longer a threat.
"There was a call approximately an hour and 25 minutes ago for a shooter in the school.
"The fire department responded collectively with sheriff's office.
"They organised together as soon as they arrived and their mission was to go in and neutralise or locate and neutralize the person who had the weapon and immediately start to care for any victims they found.
"They did that successfully," he said.
The three children were rushed to the Sacred Heart Medical Center, 25km away.
One girl who was evacuated from the school said her cousin was among those injured.
"She got shot in the side and it's, we don't know if it's lodged in her spine or her colon but we know it's pretty critical," she told KHQ.
The hospital has since revealed that all students it is caring for are in a stable condition.
Washington Governor Jay Inslee said the shooting was '"heartbreaking".
"All Washingtonians are thinking of the victims and their families.
"We're grateful for the service of school staff and first responders working to keep our students safe," he said in a tweet.
Every other high school in the district was put on lockdown as a precaution shortly after the shooting. They are now safe.
Terrified parents flocked to the school immediately after news of the shooting spread.
Spokane Police immediately closed the highway which approaches the school, forcing some parents to abandon their cars and walk more than a mile to get to their children.
Shortly after 12pm, two hours after the shooting, police began reuniting students with parents who had gathered outside.