In injury time of United's 2-1 Premier League victory at Anfield on Sunday, the Slovakia international - chasing a throughball - stood on the right leg of De Gea as the Spaniard gathered the ball.
No action was taken at the time by referee Martin Atkinson, but the FA has decided to punish Skrtel retrospectively for violent conduct.
An FA statement read: "In Premier League matches, if an incident has not been seen by the match officials, a three-man panel of former elite officials will be asked by The FA to review the footage independently of each other.
"They will then advise what, if any action, they believe the match referee should have taken had it been witnessed at the time.
"For an FA charge to follow, all three panel members must agree it is a sending-off offence.
"In this instance, the decision by the panel was unanimous."
Should he be found guilty, Skrtel will likely face a three-match ban and a spell on the sidelines alongside his captain Steven Gerrard, who was sent off within 38 seconds of coming on as a half-time substitute for stamping on Ander Herrera.
