A months-long international investigation led to the 19-year-old suspect, who used "advanced camouflage technologies" to cover his tracks, police spokesman Micky Rosenfeld said.
The suspect holds dual American-Israeli citizenship, an Israeli security official told CNN. He was arrested in southern Israel after an undercover investigation with the FBI.
The threats were made against sites in the United States, Australia and New Zealand. In one case, an airline had to make an emergency landing, Rosenfeld said.
Israeli police are still trying to determine the teen suspect's motive. The FBI confirmed the arrest and said in a statement it could not provide further information.
JCC Association of North America President and CEO Doron Krakow said he was "gratified" by the arrest but added that he was "troubled" by the suspect's background.
"We are troubled to learn that the individual suspected of making these threats against Jewish Community Centers, which play a central role in the Jewish community, as well as serve as inclusive and welcoming places for all, is reportedly Jewish," Krakow said.
Other leaders of Jewish institutions, including the Anti-Defamation League, said they were "relieved" by the arrest.
"While the details of this crime remain unclear, the impact of this individual's actions is crystal clear: These were acts of anti-Semitism," ADL CEO Jonathan Greenblatt said in a statement. "These threats targeted Jewish institutions, were calculated to sow fear and anxiety and put the entire Jewish community on high alert."
"We're very relieved that the person was caught," Rick Zakalik, executive director of the JCC of Greater Buffalo, told CNN. "It's obviously a very disturbed young man, and I pity his parents."
US Attorney General Jeff Sessions commended the FBI and Israeli National Police for their work on the case.
"Today's arrest in Israel is the culmination of a large-scale investigation spanning multiple continents for hate crimes against Jewish communities across our country," Sessions said in a statement. "The Department of Justice is committed to protecting the civil rights of all Americans, and we will not tolerate the targeting of any community in this country on the basis of their religious beliefs."
The teenager has a history of behavioral issues and was diagnosed with an inoperable brain tumor when he was 14, his attorney, Galit Besh, told CNN.
The suspect's father was detained and questioned in connection to the investigation, Besh said.
Shiraz Biton, a neighbor in the southern Israel city of Ashkelon, said that she has seen the suspect and his family a lot. The suspect was "quiet" and "introverted" and seemed a "little strange," she said.
"He was always alone," Biton said. "Him and his laptop."
Rampant threats in US
In the US alone, more than 100 bomb threats have been made this year against Jewish community centers and schools. The threats were spread across 33 states and most came as part of five waves.
Though none of the threats was carried out, the calls and emails prompted evacuations and anxiety for many of the targets
. Several instances of vandalism of Jewish cemeteries
, though unrelated, heightened fears of anti-Semitism.
The incidents reached such a critical mass that President Donald Trump addressed the matter several weeks ago in his first speech to Congress
"Recent threats targeting Jewish Community Centers and vandalism of Jewish cemeteries ... remind us that while we may be a nation divided on policies, we are a country that stands united in condemning hate and evil in all its forms," Trump said.
Most of the bomb threats were believed to have been made by one person
using technology to disguise his voice to sound like a woman's, while the other threats likely were made by copycats, a New York police official said earlier this month.
The calls were "unprecedented" for their methodical approach and sophistication, said Paul Goldenberg, who advises Jewish organizations on security as national director of the Secure Community Network.
"These masking technologies are very effective," he previously told CNN.
Previous suspect arrested
On March 3, a fired reporter was arrested and accused of making at least eight of the bomb threats.
Juan Thompson, who was fired from the online news site The Intercept for fabricating quotes
, made the threats in an attempt to intimidate someone after their romantic relationship ended
, authorities said.
But the accusation against Thompson accounted for just a small fraction of the more than 100 bomb threats received by Jewish institutions this year, according to data from the JCC Association of North America.