Puncheon, who played for Warnock during a loan spell at QPR in 2011, posted a series of comments on Twitter last month that included allegations over the way Warnock selected his teams, as well as an attack on his training regime.
The incident came after the midfielder had missed a penalty during Palace's defeat to Tottenham, with an attempt that led to criticism from Warnock in his role as a pundit on talkSPORT.
Although Puncheon went on to delete his tweets concerning Warnock, the FA have opted to act.
A statement on Monday read: "It is alleged that in posting these comments, Puncheon failed to act in the best interests of the game, and/or acted in a manner which was improper, and/or used abusive and/or insulting words in contravention of FA Rule E3[1].
"Puncheon has until 6pm on Thursday 27 February 2014 to respond to the charge."
Puncheon has made 25 appearances for Palace in all competitions this season, scoring three goals, and made his move from Southampton permanent during the January transfer window.
Following the player's attack, Warnock told the Telegraph: "He’s made comments that I know nothing about and if it’s been suggested that I’ve done anything untoward then I can confirm that I most certainly have not.
"The matter is being addressed with him directly now on my behalf."
‘The pure simplicity of the way Slot has managed the squad is probably the biggest thing I could say about him. It’s not broken, so let’s get on with it’: Liverpool legend full of admiration for Jurgen Klopp's successor at Anfield
‘I trained at Spurs and thought they’d give me a chance. But I received a letter thanking me but saying they didn’t think I was good enough – I was gutted’: How Tottenham missed out on signing Wales legend John Toshack
