The 79-year-old rocker will take to the Pyramid Stage with his band The Chrome Hearts on Saturday but those watching on TV will see Charli XCX's performance on The Other Stage which takes place at the same time.
A spokesperson for the BBC said: "On Saturday on BBC iPlayer, our Glastonbury Channel and five streams for the main stages will bring a range of live performances to audiences.
"At the artist's request, we won't be livestreaming Neil Young's set. Our plans, including those for our TV highlights shows and on-demand coverage, continue to be finalised right up to and during the festival."
The announcement comes after Young threatened to pull out of Glastonbury earlier this year due to BBC's involvement as he bemoaned how the UK festival had fallen "under corporate control".
The veteran rocker wrote in an open letter on his website in January: "The Chrome Hearts and I were looking forward to playing Glastonbury, one of my all time favourite outdoor gigs. We were told that the 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. 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."
However, Young made a U-turn on his Glastonbury boycott two days later after suggesting that he had received false information about the festival.
"Due to an error in the information received, I had decided to not play Glastonbury Festival, which I always have loved.
"Happily, the festival is now back on our itinerary and we look forward to playing!"
Young was opposed to the BBC broadcasting his set when he previously headlined the festival in 2009 as his management wanted to limit the number of songs shown on TV in order to preserve the "mystery" of the performance.
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