According to the Crossrail statement, the skulls were found 20-feet underground, beneath a 16th century Bedlam burial ground where 3000 skeletons will be removed in a major dig next year.
Archaeologists have said the skulls may be victims of Boudicca's revolution, The Guardian reported.
"This is an unexpected and fascinating discovery that reveals another piece in the jigsaw of London’s history," Lead archaeologist Jay Carver said.
"This isn’t the first time that skulls have been found in the bed of the River Walbrook and many early historians suggested these people were killed during the Boudicca rebellion against the Romans.
"We now think the skulls are possibly from a known Roman burial ground about 50 metres up river from our Liverpool Street station worksite. Their location in the Roman layer indicates they were possibly washed down river during the Roman period."
