Skrtel stepped on de Gea’s right leg as he challenged aggressively for the ball in the final seconds of stoppage-time during United’s 2-1 win at Anfield on Sunday.
The FA said in a statement the incident was not seen by the officials, but was caught on video.
The Slovakia centre-back has until 1800 GMT on Tuesday to respond to the charge.
If he were found guilty Skrtel would face a three-match ban, ruling him out of the Premier League matches against Arsenal and Newcastle and the FA Cup quarter-final replay at Blackburn.
The Reds will already have to cope without Steven Gerrard, who was sent off less than a minute after coming on as a half-time substitute for a stamp on United’s Ander Herrera.
The defeat left Liverpool five points behind bitter rivals United in the race to qualify for the Champions League via a top four finish in the Premier League.