The green bottle, which is about 15cm (5.9in) tall, was probably used in the 1700s to ward off evil spells cast by witches, researchers believe.
The witch bottles were usually filled with fingernails, hair and even urine.
The relic was found during a project to restore the Old Magnus Building for use as a museum and visitor centre.
Archaeologist Will Munford, from Pre-construct Archaeological Services of Lincoln, said :"Finding this very fragile bottle in one piece supports the idea that it was carefully placed in the ground.
"Perhaps it was buried during the construction of the Georgian part of the Old Magnus Building, but we can't be certain.
"It is the first time we have encountered a suspected witch bottle, but we did find a probable witching shoe - which had a similar purpose - in Worlaby, Lincolnshire.
"We often forget that people were very superstitious - it was part of their everyday lives.
"They thought that secreting such personal objects would offer protection from malign forces."
A witch bottle was found in the foundations of a house in Navenby in Lincolnshire in 2005
- They often contained pins, fingernails or urine and were used to ward off evil spirits
- The bottles were usually made of stoneware or glass but sometimes old inkwells or candlesticks were used
- The most famous witch trials in Britain took place at North Berwick, in Scotland, in 1591 and Pendle, Lancashire, in 1612
As many as 300 people were executed for witchcraft in eastern England between 1644-46, even though the laws against witchcraft were repealed in 1736.
Old Magnus Building project manager Bryony Robins from Newark and Sherwood District Council said the bottle would be displayed at the National Civil War Centre when it opened in 2015.
"It's a fascinating object and part of the history of Newark. If it is a witching bottle, it tells us a great deal about how people once viewed the world," she said.
BBC News. 2014. “Witch bottle found during Newark Civil War Centre dig”. BBC News. Posted: October 20, 2014. Available online: http://www.bbc.com/news/uk-england-nottinghamshire-29685608