Kennedy, then 28, predicted "Hitler will emerge from the hatred that surrounds him now as one of the most significant figures who ever lived".
"He had in him the stuff of which legends are made," he continued.
Kennedy wrote the entry in the summer of 1945 after touring the German dictator's Bavarian mountain retreat.
It is thought by historians to be the only diary ever kept by the 35th US president.
He wrote that Hitler "had boundless ambition for his country which rendered him a menace to the peace of the world, but he had a mystery about him in the way he lived and in the manner of his death that will live and grow after him".
The 61-page diary was kept by Kennedy around four months after Hitler committed suicide.
At the time, the young American was touring Europe as a newspaper reporter after finishing his military service aboard a ship in the Pacific Ocean.
He gave Ms Henderson the diary in order to inform her of his views on foreign policy and national security, she said.
In a description of the auction, she wrote: "When JFK said that Hitler 'had in him the stuff of which legends are made', he was speaking to the mystery surrounding him, not the evil he demonstrated to the world."
"Nowhere in this diary, or in any of his writings, is there any indication of sympathy for Nazi crimes or cause," she continued.
The diary also contains JFK's thoughts about the British election and Winston Churchill, who Ms Henderson called his "idol".
The winning bid is expected to be around $200,000 (£160,000).
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