The Iron Age soutterrain was revealed during the digging of the foundations for the property in Ness.
Local archaeologists, husband and wife team Chris and Rachel Barrowman, are recording the soutterrain.
Mr Barrowman said theories on the purpose of the stone-lined, flat stone-roofed structures included storing food.
He told the BBC: “They are usually associated with what are known as Atlantic roundhouses, or wheelhouses, of the later Iron Age.
“If this one was associated with a roundhouse it is likely to have been cleared away by now.”
Mr Barrowman said the well-preserved structure is the sixth to be recorded in the area.
The soutterrain would most likely be filled in and covered over to preserve the archaeology following a full survey, the archaeologist said.
Construction of the new house would then continue as normal.
However, the local authority archaeologist is due to liaise with the islander building the house on the way forward.