Tigers players surrounded referee Mark Clattenburg after Arsenal full-back Kieran Gibbs was only booked for fouling Lazar Markovic when the Hull winger was clear on goal.
That resulted in a Football Association misconduct charge, which the club have admitted.
"Hull City have been fined £20,000 after admitting an FA misconduct charge and accepting the standard penalty," said a statement from the FA.
"In the 55th minute of the game against Arsenal on February 11 2017, the club failed to ensure that its players conducted themselves in an orderly fashion, contrary to FA Rule E20 (a)."
Meanwhile, Clattenburg has announced that he will be leaving the Premier League after 12 years to work in Saudi Arabia.
The 41-year-old Englishman's move was confirmed by Professional Game Match Officials Limited (PGMOL), the organisation which provides and trains officials for the Premier League, English Football League and Football Association.
In a statement, PGMOL said: "Mark is a talented referee, he has been a great asset to the English game and hopefully an inspiration to those who want to get into refereeing at the grass roots of the game.
"We understand this is an exciting opportunity for Mark as well as further underlining what high esteem English match officials are held throughout the world game."