Archaeologists from the University of Sheffield made the discovery at Thornton Abbey near Immingham and have called it "extremely rare".
They said the presence of such a large burial site at the abbey - where more than half of the skeletons were children's ones - suggests the community was overwhelmed by the Black Death and left unable to cope with the number of people who died.
The Black Death was one of the worst pandemics in human history. It devastated European populations from 1346 to 1353 and resulted in the deaths of an estimated 75 to 200 million people.
The disease is documented to have reached Lincolnshire in the spring of 1349.
The team said they sent teeth samples from the skeletons to McMaster University in Canada where ancient DNA was successfully extracted from the tooth pulp. DNA tests revealed the presence of Yersinia pestis, the bacterium responsible for the plague.
Dr Hugh Willmott, from Sheffield University's Department of Archaeology, said: "The finding of a previously unknown and completely unexpected mass burial dating to this period in a quiet corner of rural Lincolnshire is thus far unique, and sheds light into the real difficulties faced by a small community ill-prepared to face such a devastating threat."
The project will feature on the BBC's Digging For Britain programme on December 13.