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.