Los Angeles shut more than 1000 public schools due to the threat of an attack, which federal officials later said was most likely a hoax.
The emailed threat was "routed through Germany" but likely more local in origin, authorities said.
Officials asked parents to keep all the district's 643,000 students at home, and those who were already at school were sent home.
The unprecedented move at the second-largest public school system in the United States left students and their families scrambling to make last-minute alternative arrangements and drew wide criticism.
The head of the New York City Police Department said officials there received a similar threat and indicated the Los Angeles closings may have been an "overreaction."
The city's police commissioner, William Bratton, said the threat received on Tuesday was not considered credible. He said he believed that email was "almost exactly the same" as the one sent to Los Angeles.
But Los Angeles police chief Charlie Beck said it was "irresponsible" to criticise when you did not have the responsibility of safeguarding three-quarters of a million lives.
He said the email mentioned assault rifles and machine pistols and implied the use of explosives. He said that officers would search all of the district's campuses.
The threat came less than two weeks after a married couple inspired by Islamic State militants shot dead 14 people in San Bernardino, California, about 100 km east of Los Angeles.
The Los Angeles school district regularly receives threats, but this one stood out for its scale, schools Superintendent Ramon Cortines said.
"This is a rare threat ... It was not to one school, two schools or three schools, it was many schools," Mr Cortines told reporters at a press conference that began shortly before schools were to begin opening. "I am not taking the chance of taking children any place into the building until I know it's safe."
Officials said they were not aware of any other threats to schools outside the district, adding that they would issue additional details on the threat later in the day.
The United States has suffered repeated deadly attacks in schools in recent years, typically carried out by gunmen.
The deadliest attack in the past decade occurred at Virginia Tech, where a shooter killed 32 people. The second deadliest was the 2012 massacre at Sandy Hook Elementary School in Newtown, Connecticut, which left 20 young children and six educators dead.
- Reuters / BBC