Hughes was sent to the stands in Stoke's 5-1 defeat to Newcastle United on December 26, having kicked a ball onto the pitch in frustration following the dismissal of Glenn Whelan.
The Welshman later admitted to being in the wrong and has now been sanctioned.
A statement from the FA on Thursday confirmed Hughes' punishment.
It read: "Stoke City manager Mark Hughes has been fined the standard penalty of £8,000 after he admitted an FA misconduct charge.
"The charge was that his behaviour in or around the 40th minute of Stoke's game against Newcastle United on 26 December 2013 amounted to improper conduct."