Israeli PM Netanyahu and his wife Sara saw them off, just an hour after Air Force One landed at Ben Gurion Airport, before departing in a limousine.
In Jerusalem, the couple is expected to visit the Old City, the Church of the Holy Sepulcher and the Western Wall, before Trump holds talks with Netanyahu.
Mr Trump will hold talks with both Israeli and Palestinian leaders during the course of his two-day stop.
The president has called an Israeli-Palestinian peace agreement "the ultimate deal", but has been vague about what form it should take.
He has said he prefers to leave it to both sides to decide between them in direct talks. On his arrival in Tel Aviv, Mr Trump said he hoped the US and Israel could work together in an era of "harmony, prosperity and peace".
Mr Trump's flight between Saudi Arabia and Israel is likely to have been the first between the two countries, that have no diplomatic relations.
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