Dozens of Palestinian supporters attacked Cowell on Twitter for the donation, which he made at a gala in Beverley Hills.
Alongside an image of four dead Palestinian children on stretchers, one Twitter user wrote: 'You have blood on ur hands.'
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SIMON COWELL RELEASES STATEMENT ADDRESSING GAY RUMOURS
Another user, calling themselves Ronnie, said: 'these children's last memory was of the beach. Unlike you, they're no #friendsoftheidf.'
Twitter users were referring specifically to the young boys from one family who were killed by Israeli fire whilst playing on the beach in Palestine last week, although there have now been hundreds of deaths from bombings in the last fortnight.
The Palestinian death toll has now passed 609 people in the past two weeks, including over 100 children.
Israel has lost 29 individuals, mainly soldiers.
Cowell has increasingly embraced the Jewish faith since becoming involved with Lauren Silverman, a practising Jew.