The disease, caused by Vitamin D deficiency linked to lack of sunlight, can lead to weak and deformed bones.
It was identified in the remains of a Neolithic woman who had been buried on the Scottish island of Tiree.
Researchers from Durham and Bradford Universities made the discovery. Until now, the earliest case of rickets in Britain dated from the Roman period.
The skeleton was discovered along with at least three other burials during an amateur excavation on Tiree in 1912.
Only one of the skeletons was taken off the island, and is now part of the Hunterian collection at Glasgow University.
The skeleton was always assumed to date from the same period as a nearby Iron Age settlement.
However, recent radiocarbon dating by scientists from Bradford and Durham Universities showed the skeleton was actually from between 3340 and 3090 BC - in the Neolithic period.
Their examination also identified rickets in the woman's badly-deformed bones.
The bones show a number of deformities in the breastbone, ribs, arms and legs.
These would have left the woman pigeon-chested with misshapen limbs - all characteristic of the disease.
Professor Ian Armit, from Bradford University, said: "The earliest case of rickets in Britain until now dated from the Roman period, but this discovery takes it back more than 3,000 years.
"There have been a few possible cases in other parts of the world that are around the same time, but none as clear cut as this.
Professor Armit said it was unclear how the woman would have developed rickets.
"Vitamin D deficiency shouldn't be a problem for anyone exposed to a rural, outdoor lifestyle, so there must have been particular circumstances that restricted this woman's access to sunlight as a child," he said.
"It's most likely she either wore a costume that covered her body or constantly remained indoors, but whether this was because she held a religious role, suffered from illness or was a domestic slave, we will probably never know."
The research team's findings have been published in Proceedings of the Prehistoric Society.
The earliest known case of rickets in the UK has been identified in a 5,000-year-old skeleton found in Scotland.