The 74-year-old came out of retirement in February for a second spell as boss of the Terriers to save them from relegation to the Championship.
He originally said his heart "couldn't take" a full season with Town, but he later confirmed that he would stay for another year.
However, despite winning their past two matches, Terriers chief executive Jake Edwards said Stoke City would be Warnock and assistant Ronnie Jepson's last game.
Mr Jepson said the club are "ready to make a longer-term managerial appointment" and that "he'd like to express huge gratitude for everything [Warnock and Jepson] have accomplished over the past seven months".
He added: "We have discussed... the timing of it with Neil, and after spending time with his coaching staff he has graciously agreed now is the time for that to happen."
At a press conference, Warnock said that they'd "actually done what we set out to do really".
He added: "If you're not wanted, you want to go straight away.
"I don't mean that how it maybe sounds - we always said we'd be straight with each other and that's what we've done.
"I'm disappointed and I'll miss my players."
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