Trial trenches have been dug in a field on the outskirts of South Queensferry on land reserved for the planned Forth Replacement Crossing (FRC).
Archaeologists plan further excavations to confirm what they believe is an early version of a croft or small farm.
The discovery is not expected to affect construction of the new crossing.
Edinburgh-based Headland Archaeology (UK) Limited, which is conducting the dig, has also found what it believes to be the remains of a circular house and uncovered a number of items, including pieces of Neolithic pottery and a flint arrowhead.
The rare finds offer a glimpse of how the land was used 4,000 years ago.