Biden has said his songs hold deep meaning for him and John, CNN reported, asked the White House if he could perform.
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The event, dubbed "A Night When Hope and History Rhyme," is part of a collaboration with A&E Networks and The History Channel, which are paying for the event, according to the White House. The title of the event is a quote from Irish poet Seamus Heaney that Biden frequently uses in speeches and remarks, including when he accepted the Democratic nomination in 2020.
The event, before Cabinet secretaries and 2,000 invited guests, is to honor John's life and work, according to the White House, as well as to commemorate "the everyday history-makers in the audience, including teachers, nurses, frontline workers, mental health advocates, students, LGBTQ+ advocates and more."
The president, in brief remarks to kick things off, said he and the first lady invited John to come and perform at the White House when he was stopping in DC on his farewell concert tour. He spoke about how with his music, John helped so many find their voices and he changes so many lives.
"On behalf of the American people, thank you - and I sincerely mean this - for moving the soul of the nation," the president said.
John came out and seemed to be impressed by the surroundings.
"I have played in some places before that have been beautiful, but this is probably the icing on the cake," John said as he sat down at his piano.
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John has a concert scheduled Saturday night at nearby Nationals Park, part of his "Farewell Yellow Brick Road Tour." The 300-plus world tour dates are a farewell to his fans all over the world, according to the "Crocodile Rock" singer, part of a nearly 50-year career in music.
It's not the first time the singer has been at the White House. In 1998, President Bill Clinton invited him to play at a state dinner for then-U.K. Prime Minister Tony Blair, along with Stevie Wonder.
Biden has said that John's music has comforted his family at its most painful moments.
In his 2017 memoir, "Promise Me, Dad: A Year of Hope, Hardship, and Purpose," Biden recounted visiting his son Beau in the hospital one night shortly before Beau died of brain cancer. John had been at the White House earlier that day, Biden wrote.
When he reached Beau's bedside that night, Biden said, he sang "Crocodile Rock" to Beau -- just as he had to Beau and his other son, Hunter, many years before, after Biden's wife and daughter were killed in a car accident.
"The words came back like it was yesterday, but after the first few lines I started to get emotional and wasn't sure if I could go on," Biden wrote. "Beau didn't open his eyes, but I could see through my own tears that he was smiling. So I gathered myself and kept at it, for as much of the song as I could remember."
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In addition to his music, John has also been lauded for his work as an AIDS activist, having testified numerous times on Capitol Hill in support of AIDS funding. To date, according to its website, the Elton John AIDS foundation has raised over $600 million since its inception in 1992.
John also has another presidential fan -- former President Donald Trump -- who reportedly wanted the Grammy Award winner to play at his inauguration, but John declined.
Trump frequently plays John's music at his rallies and infamously reacted to the news of the death of Supreme Court Justice Ruth Bader Ginsburg as "Tiny Dancer" blared in the background.
Trump even dubbed North Korean leader Kim Jong Un "Little Rocket Man" in what appears to be a reference to John's song, "Rocket Man." The singer also performed at Trump's wedding in 2005 to his current wife, Melania.
ABC News' Karen Travers contributed to this report.