The snuff box may have been carried by Burke when he carried out the infamous murders with William Hare and was found in his pocket when he was searched by a warder at the Calton Jail.
On the underside, the Irishman has scratched his own details: "W Burke Shoemaker West Port Edinr".
Unseen in public for nearly 200 years, the snuff box will be among the highlights of the second day of Bonhams' Scottish Sale, on Friday, when it is estimated to fetch £2000-3000.
Hamish Wilson, Bonhams' specialist, said: "This is an incredibly important part of Edinburgh's - and Scotland's - social history.
"To know the details of how it was taken from William Burke - one of the most notorious figures in Scotland's dark history - is remarkable.
"This is something Burke would have carried every day for many years and was with him when he was apprehended and taken to the Calton Jail.
"It looks like the warder who searched his pockets has simply kept the contents and passed this snuff box onto his friend, possibly as a memento. It has come down to the current owner by inheritance.
"It has a macabre feeling to it. It will appeal very much to historians, snuff mull collectors and all sorts of institutions and museums -- I would love for it to be on public view."
The snuff box is thought to have been made by Burke himself. It consists of bone with a hinged cover and brass collar. It has an uninscribed plaque but the base is inscribed by Burke.
Accompanying it is a note signed in May 1878 by one time owner John Mackie, of 4, Great King Street Edinburgh, which reads: "Made and used by William Burke, the notorious murderer who was executed in Edinburgh in 1829. After his apprehension he was taken to the Calton Jail, he was searched by a Warder and amongst other things which were in his pockets was this box.”
William Burke arrived in Edinburgh from Donegal as a shoemaker but worked as a labourer on the Union Canal. He met fellow Irishman William Hare in 1826 when he moved from Leith to a boarding house in Tanner's Close, in the city's West Port. The pair would become infamous for the "West Port Murders" - the killing spree they undertook to provide bodies for anatomy classes in the Edinburgh Medical School.
Burke was held at the Calton Hill jail until 28 January 1829 when he was taken to the Scaffold. When he arrived, a huge crowd is said to have given "three triumphant cheers". When his body was cut down, police had to restrain members of the crowd from trying to exact revenge by tearing it to pieces.
More than 21,000 people were later admitted to see the body before it was dissected at the University of Edinburgh. Burke's skeleton and death mask are still exhibited in the university's Anatomical Museum.