Members of the American Studies Association, the largest group devoted to the interdisciplinary study of American culture and history, voted on Sunday by two-thirds to endorse the boycott.
Various organisations across the world campaign for academic and cultural boycotts of Israel to protest against its more than 40-year occupation of Palestinian territory.
But it is only the second time a US academic organisation has voted to boycott Israeli universities. The Association for Asian American Studies endorsed a boycott in April.
But World Jewish Congress President Ronald Lauder said the vote "shows the Orwellian anti-Semitism and moral bankruptcy of the American Studies Association."
He criticised the move as unfair and biased in the wider context of the Middle East, where civil war in Syria and uprisings in a number of Arab countries have left tens of thousands dead.
"The American Studies Association singles out the Jewish state, the one Middle Eastern country that shares American values, for opprobrium? No wonder many Americans dismiss the academy as deeply biased and disconnected with reality," Lauder said.
The World Jewish Congress is the international organisation representing Jewish communities in 100 countries.
Set up in 1951, the American Studies Association is the oldest and largest association in the United States devoted to the interdisciplinary study of American culture and history.
According to its website, it has 5,000 individual members along with 2,200 library and other institutional subscribers.
Earlier this year, renowned British physicist Stephen Hawking pulled out of a June conference hosted by Israel's President Shimon Peres on the grounds of an academic boycott.
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