Michael Ron David Kadar, 18, who has joint US-Israeli citizenship, allegedly used the internet to make hundreds of hoax calls in the US, UK, Canada, New Zealand and Australia.
Prosecutors say he often used software to disguise his voice as a woman's.
He is also accused of trying to extort money from a US senator.
Israeli prosecutors say Mr Kadar made more than 2,000 threatening calls to schools, airports, police stations and hospitals over a two-year period.
The charges against him were filed in Florida and Georgia, but the US justice ministry has said he will be tried in Israel. His motives remain unclear.
Threats to schools and planes
Mr Kadar reportedly targeted several British Jewish schools between February 2016 and March 2017.
On 28 February 2017 the Jewish Museum in London was evacuated after a bomb threat attributed to him.
The charges also include making threats to passenger planes, including British Airways flights between London and New York.
Prosecutors say that Swiss and French warplanes were scrambled to escort an El Al flight to Israel, after Mr Kadar falsely claimed a bomb was on board.
In another incident, a hoax threat from the defendant reportedly forced the diversion of a passenger plane. Those on board were evacuated using the slides, and six were injured as a result.
Mr Kadar is also accused of threatening to kidnap and kill the children of a former senior official at the Pentagon.
'He can't think straight'
The teenager, who is himself Jewish, was arrested on 23 March in the southern Israeli city of Ashkelon. The investigation had involved the FBI and police forces from several countries.
A large antenna was discovered attached to his home which prosecutors say he used to disguise his identity by using neighbours' Wi-Fi networks.
Mr Kadar's lawyer has said he suffers from a medical condition that may cause behavioural problems.
He claimed the young man has a high IQ, but the emotional intelligence of a five-year-old.
The teenager's American-born mother told Israel's Channel 2 that her son was home-schooled after he was unable to function in school due to a brain tumour.
"He's autistic," she said. "He can't control it. He can't think straight."
In the same interview, Mr Kadar's Israeli father said: "To all the Jews in America, I want to say clearly - we are very, very sorry, from the bottom of our hearts."
Last month a former journalist, Juan Thompson, was arrested in connection with several of the threats.
Investigators say that 31-year-old suspect's alleged calls were part of a bizarre campaign against a former girlfriend.