The pub, which calls itself the most haunted in the city, noticed the skull – attributed to Elizabeth Johnson – was missing the following day.
Elizabeth was hanged in August 1800 after being found guilty of using a forged £1 banknote – worth £89 today – with intent to defraud the Bank of England.
The 518-year-old pub put out an appeal on social media, revealing how Elizabeth had been “removed” from her “resting place”.
Social media users were initially concerned that the pub was displaying human remains in the first place – causing the pub to respond by claiming that the skull was a replica.
The Golden Fleece posted their appeal to bring Elizabeth “back to her rightful home” on Monday afternoon, writing: “Help needed. Unfortunately over the course of last night/today someone has taken it upon themselves to remove Elizabeth from her resting place.
“This is beyond us why anyone would want to take her and we sincerely hope the culprit had a lapse of judgement and will return her to us ASAP.
“We are currently looking through all our CCTV in order to hand it over.
“Please contact us if you have any information on her whereabouts to bring her back to her rightful home.”
They later updated the post, adding: “This is obviously not Elizabeth’s real skull.
“We believe she frequented the Fleece when it was an Inn and this was made and donated to the owner at the time, although the entire story is not fully known.
“Thank you all for your comments, we appreciate your concern but are just trying to be reunited with our property, thanks.”
The post has been shared over 600 times and almost 200 comments from shocked Facebook users.
John Owens said: “Unbelievable. Hope Elizabeth is returned to her rightful resting place ASAP.
“Someone must know which lowlife took her.”
Claire Joy Salter said: “My god why would anyone think it’s a great idea to take her.
“No morals, no respect, hope she does her worst and makes their life hell so they return her.”
Caley Sampson said: “This has knocked me sick. Why on earth would anyone do something like that?
“Some people (I use that term very loosely) have absolutely no morals whatsoever. I really hope you get her back.”
Scott SH said: “Why would you want to steal a skull? Some really weird people about.”
And Ruby Florence Lea wrote: “I hope she haunts whoever’s taken her.”
Elizabeth Johnson was a frequent visitor to the Golden Fleece pub during her lifetime.
She was found guilty of “uttering a forged £1 bank note with intent to defraud the Bank Of England in the parish of Pontefract on June 7th 1800”.
She was subsequently hanged at Knavesmire in York on 23 August 1800.
This was believed to be the last execution to take place there.
The Golden Fleece has a long history of spooks and spectres, with fifteen separate sightings of ghosts wandering around the premises.
One of these is supposedly Lady Alice Peckett – the wife of John Peckett – former owner of the establishment and mayor of York in the early 1700s.
Other alleged apparitions include a 16th-17th century redcoat called One Eyed Jack, a WWII Canadian airman and even Roman soldiers in the cellar.