The huge graveyard was found during excavations beneath the Old Divinity School at St John's College in the university as part of recent refurbishments.
The mass cemetery, which was far larger than the small burial ground which archaeologists had expected, contained around about 1,300 burials, including about 400 complete skeletons.
The bodies, which mostly date from a period spanning the 13th to 15th centuries, are burials from the medieval Hospital of St John the Evangelist which stood opposite the graveyard until 1511, and from which St John's College takes its name.
Craig Cessford, from the university's department of archaeology and anthropology who led the dig, said it was one of the largest finds of its kind in the UK.
"Evidence for clothing and grave-goods is rarer than at most hospital cemeteries. This is principally because this was a purely lay graveyard with no clerics present," he said.
"Items were found in graves that might represent grave- goods, but their positions were ambiguous and it is equally possible that they represent residual material from earlier activity at the site," he said.
Most of the bodies were buried in neatly laid-out rows between gravel paths. Seeds from flowering plants suggested the site was similar to cemeteries today.
However, majority of people were buried without coffins and many were not shrouded, suggesting the cemetery was primarily for the poor. Only a handful of grave goods, such as jewellery or other personal items, were found.
It had been rumoured the cemetery was linked to the Black Death, but Cessford's team found no evidence of the disease when the skeletons were analysed.
The remains will be stored by Cambridge Archaeological Unit, enabling further research to take place in the future.