Following Sunday's dramatic 4-3 win over Tottenham he appeared to call into question the integrity of Tierney and suggested he "had history" with the club.
In announcing the charge on Tuesday the FA said: "It is alleged that the manager's comments regarding the match official during post-match media interviews constitutes improper conduct in that they imply bias, and/or question the integrity of the referee, and/or are personal/offensive, and/or bring the game into disrepute."
Klopp, who has until Friday to respond, has said he expects to be punished.
After his side's late winner, Klopp ran down the touchline to celebrate in front of fourth official John Brooks and received a yellow card from Tierney.
"The whole situation shouldn't have happened at all. It was out of emotion, out of anger in that moment. That's why I celebrated the way I celebrated," Klopp said earlier on Tuesday.
"I didn't say anything wrong. I couldn't get close to the fourth official and I didn't want to get close to him.
"Paul Tierney came over and I didn't expect a red card I expected a yellow. He said to me: 'For me it's a red card,' but he gave me a yellow.
"After the game I tried to calm down and didn't properly. I said (in TV interviews): 'What he said to me was not OK'. I opened the box which I didn't want to open.
"The rest was things I said about how I felt in that moment and Paul Tierney doing our games. I'm not a resentful person but these things which happen in the past happens, not intentionally but they are there.
"Obviously the refs are really angry about what I said. I did a lot of things that day but I didn't lie."
Klopp said after the game that he did not know what the official "has against us".
Klopp added: "With all the things I maybe expect a punishment. Refs think I questioned their integrity, which if I am sitting here now calm, I don't do. We have to wait to see what they come back with."
Shortly after the Spurs game the Professional Game Match Officials Limited said, "having fully reviewed the audio of referee Paul Tierney from today's fixture, we can confirm he acted in a professional manner throughout including when issuing the caution to the Liverpool manager... we strongly refute any suggestion that Tierney's actions were improper."
