The indictments were filed in Orlando, Florida and Athens, Georgia.
In the indictment filed in Orlando Federal Court, the young man has been accused of making 245 threatening phone calls, the majority to Jewish community centers and schools in Florida. The threats were made primarily from January to March and included dozens of messages graphically describing the deaths of children.
According to the indictment, the suspect used an online call service to disguise his voice to that of a woman in order to help conceal his identity.
In an attempt to further conceal his identity, the suspect paid for the calls using Bitcoin, which provides relative anonymity.
In what would appear to amount to particularly damning evidence, the defendant recorded all the conversations himself and kept them in files arranged in his home, along with news stories describing police responses to the threats.
The suspect has been charged with 28 counts of making threatening calls and transmitting false information to the police.
In a separate indictment filed in Georgia, the young man is charged with three other counts of making threatening calls, transmitting false information, and internet harassment.
The indictment links the young man to several cases in which the authorities were called upon to respond to emergencies that turned out to be fabricated.
One of them describes a case in January, in which the Georgia University police received a phone call about a home invasion of the house that turned out to be false.
The defendant, whose name is being withheld in Israel pending a formal indictment, has dual American-Israeli citizenship.
According to records from Florida Federal Court, he has no lawyer representing him in the US.
In an interview with Channel 2 News, the defendant's mother said that her son was home-schooled after he was unable to function in school due to a brain tumor.
"He's autistic," she said. "He can't control it. He can't think straight."
The young man's attorney in Israel offered a similar assessment, telling reporters that despite having a high IQ, the young man had the emotional intelligence of a five-year-old.
The US Justice Department has not said whether it will seek his extradition.
Reuters contributed to this report.
(Translated and edited by Fred Goldberg)