The 79-year-old singer announced earlier this week that he and his band The Chrome Hearts would not be playing Worthy Farm because of the BBC's involvement at the festival but has now made a U-turn as he blamed "an error in the information I received" for his previous stance.
In a statement posted on his website, Neil said: "Due to an error in the information received, I had decided not to play the Glastonbury Festival, which I have always loved.
"Happily, the festival is now back on our itinerary and we look forward to playing. Hope to see you there."
View this post on Instagram A post shared by Emily Eavis (@emily_eavis)
Glastonbury organiser Emily Eavis is delighted with the Rockin' in the Free World artist's change of heart.
She wrote on Instagram: "What a start to the year!
"Neil Young is an artist who's very close to our hearts at Glastonbury. He does things his own way and that's why we love him.
"We can't wait to welcome him back here to headline the Pyramid in June."
It is not clear whether Young's decision will mean that his set will be televised after he only allowed the BBC to screen a short portion of his two-hour headline set when he last played at the festival in 2009.
Neil previously suggested that he had turned down the chance to perform at the world-famous festival as he bemoaned how the event had fallen "under corporate control".
He originally said in a note on his website: "The Chrome Hearts and I were looking forward to playing Glastonbury, one of my all-time favourite outdoor gigs. We were told that BBC was now a partner in Glastonbury and wanted us to do a lot of things in a way we were not interested in. It seems Glastonbury is now under corporate control and is not the way I remember it being. Thanks for coming to see us the last time!
"We will not be playing Glastonbury on this tour because it is a corporate turn-off, and not for me like it used to be. Hope to see you at one of the other venues on tour."
The BBC is the exclusive broadcast partner of Glastonbury and has worked closely with the festival since 1997.
The rest of this year's music acts are yet to be announced but Sir Rod Stewart has been confirmed for the coveted teatime legends slot on the Sunday.
with PA
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