The remains, thought to be more than 10,000 years old, were found during excavation works in preparation for building a new bridge across the Firth of Forth, The Independent newspaper reported.
A large oval pit almost 23 feet in length was filled with more than 1,000 flint artifacts including tools and arrowheads, archaeologists said.
A number of holes around the perimeter of the pit would have held wooden posts to support the walls and roof, probably covered with turf, they said.
The site has been dated to the Mesolithic period, around 10,252 years ago.
"The radiocarbon dates that have been taken from this site show it to be the oldest of its type found in Scotland," Rod McCullagh, a senior archaeologist at Historic Scotland, said.
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