The tiny silk and leather shoes were left to the University of Aberdeen as part of a collection by Robert Wilson, a doctor who graduated from the university before travelling the world.
Mr Wilson died in 1871 and clothes, jewellery and objects he collected while working as a ship's surgeon with the East India Company were passed to the university's museum.
The history of the slippers was uncovered by assistant curator Louise Wilkie, who started cleaning and sorting Mr Wilson's collection.
She said: "In a list of the objects donated by Wilson is the description of 'A pair of slippers - Pauline, Rome Jan 20th 1824'. The same inscription is on the base of the slipper.
"I began to look at other archival material held by the university and found that Wilson had a friendship with Princess Pauline Borghese, the sister of Napoleon Bonaparte.
"Letters from him to Pauline show a close friendship and in his diary he describes how she spent a lot of time with him travelling in Italy and gave him many gifts, including a ring which is also held in the museum collections."
The decorative shoes are equivalent to a UK children's size two and measure just 40mm across the toes. The dimensions of the slippers fit with descriptions of Princess Pauline, who was said to have been very small.
Ms Wilkie said: "The relationship between Wilson and Princess Pauline can only be speculated upon, however records do indicate some form of attraction and attachment.
"In his diary he wrote 'I passed a fortnight in the vicinity of Pisa with the Princess Borghese in a state of almost perfect seclusion and afterwards accompanied her to the Baths of Lucca'.
"It seems she spent a great deal of time with him in Italy and a close friendship developed. He kept the gifts she had given him for life and then they passed to the university collections."
The Princess, who was the youngest sister of Napoleon, was a colourful character and became royalty when she wed Prince Camillo Borghese, one of the richest men in Italy, in 1803. The marriage ended a short time later and Pauline spent her later years in the company of Mr Wilson.
The slippers and ring she left to him are now going on display for the first time at the university's King's Museum.
Neil Curtis, head of museums at the university, said: "The university holds huge collections and many of the items given to us over the years do not have full descriptions. It was a great piece of detective work from Louise to piece together the fascinating history behind the slippers.
"We are delighted that these significant objects are now on display and can be enjoyed by the public for the first time."