The discovery was made during excavations under Tarbat Old Parish Church in Portmahomack, Easter Ross.
Also found in the man's coffin was a pair of thick woollen hose - and bits of the man's leg hair entangled in the garment.
The boots, which still had a copper alloy buckle attached, are the only kind of their type to be found intact in Scotland, with archaeologists hailing an "incredible piece of preservation".
The find dates to the 15th Century with archaeologist believing the boots belonged to an important figure in the community, which was torn apart by inter-clan violence around this time.
Cecily Spall, director of York-based Fieldwork Archaeological Services, has worked at the Portmahomack site over a number of years.
She said: "What we found was an incredible piece of preservation.
"The man had been put in a coffin wearing these clothes but the coffin at some point collapsed and everything concertinaed. There was something about that collapse that meant that oxygen was excluded, which allowed for this incredible piece of conservation."
Ms Spall is leading the Medieval Burials Project at Tarbat Discovery Centre, a museum now open in the old parish church, which was earlier the site of a former Pictish monastery.
Ms Spall said the boots were the only known surviving example in Scotland from medieval times.
She added: The boots are very, very fragile .
"Underneath the boots was the leg hose, which are really trousers with integral feet.
"They have been identified as being made from very heavy felted wool and there were signs of wear and tear.
"These were items that had been worn during the man's lifetime. They had not been put on solely for the purpose of his burial.
"The man's body had been reduced to bones but remarkably, we found hairs from his legs caught in the hose.
"Generally, people are thought to have been buried naked or sometimes in a shroud. This man was fully clothed. It could be that he was an important person in the community. Some have suggested he may have been a clergyman.
"Whatever interpretation you put on it, it is absolutely fascinating."
The woollen hose is dated to around the late 14th Century and the boots have been placed in the early 15th Century.
Radio carbon testing is due to accurately date when the man lived with further analysis to establish where he came from, what he eat and his ancestry.
Ms Spall added: "Archaeological science has moved on so much in the past 20 years that we now have the opportunity to ask all these questions."
This is the 20th year that archaeologists have worked at Tarbat Discovery Centre.
Last month, they revealed they had made a discovery of a mysterious six-headed burial which may have been linked to one of the most brutal episodes in clan warfare.
The remains of two men in their forties were found on top of each other in a single coffin under Tarbat Old Parish Church in Portmahomack, Easter Ross.
One man died from "horrific" sword injuries that removed the bottom half of his face with a second cut found above his left eye.
The second had a blade cut above his left eye with the wound inflicted around the time of death.
Unusually, the skulls of four others had been placed around the bodies in what has been described as a 'special burial'.
The skeletal remains are thought to date from the 15th Century, when Clan Ross and Clan Mackay fought out a terrifying rivalry in the area that arguably peaked with the Battle of Tarbat in the 1480s,
Then, Clan Ross cornered a raiding party of Clan Mackay with many killed in the encounter. Survivors of the attack sought sanctuary in the church, but the Rosses set fire to it, killing all those hiding inside.
A facial reconstruction of the clansman who had a cut above his left eye was created by experts at John Moores University in Liverpool
Dr Shirley Curtis-Summers of the University of Bradford, a specialist in human osteology earlier said the men's injuries suggested they were "very, very seasoned fighters."
She added that DNA analysis will help to establish whether these men were related with isotope analysis to offer
More than 170 skeletons, including those of 40 children, have been found under the church with the site spanning five key time periods.
It was first occupied during the 6th to 7th Centuries, when the land was used as a Pictish farmstead. It then became an important Pictish monastery, which was destroyed around 800AD by a Viking raid.
The monastery was replaced and by the 12th Century became a parish church with the final period spanning the 15th to 17th Century.
The Tarbat Discovery Centre was opened 20 years ago in September 1999 by HRH The Duke of Rothesay, and has since become an award-winning museum.
A spokesperson from the Tarbat Historic Trust, which runs Tarbat Discovery Centre, said: "The Tarbat Medieval Burials Project, based at Tarbat Discovery Centre, highlights what has already been achieved and continues to reap rewards for archaeologists all over the world. It is incredible to think how important the Tarbat Discovery Centre is in the world of archaeology.
"At a time when this museum along with all the other small Highland museums, are struggling to compete with newer more centralised projects for direct funding from Government, this project is putting this area back in the spotlight on a national and international level. People know us for our Pictish monastery, but these burials are from the later medieval period.
"They were excavated over a decade ago, but as research progresses they continue to reveal their stories and help us to see them as real flesh and blood people of their time. As a museum, we very much depend on income from visitors, so we very much hope that this exciting project will attract more people to visit the Centre."