"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," Professor Ian Armit, from Bradford University, said.
"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," he said.
The discovery is particularly surprising as the disease - caused by Vitamin D deficiency linked to lack of sunlight - is more commonly associated with the urban slums of Victorian Britain than with rural, farming communities, as existed in Neolithic Scotland.
"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," said Armit.
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"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," he said.
The skeleton was always assumed to date from the same period as a nearby Iron Age settlement. However, recent radiocarbon dating by a team from the Universities of Bradford and Durham showed the skeleton was from much earlier - between 3340 and 3090 BC - placing it firmly in the Neolithic period.
The skeleton is of a woman, aged between 25-30, measuring 145-150cm which is short even by Neolithic standards.
Analysis of the layers of dentine laid down in the woman's teeth during childhood enabled the team to uncover details about her life history, particularly her diet, between the ages of three and fourteen.
The changing levels of carbon and nitrogen isotopes show that she appears to have suffered from physiological stress, possibly malnutrition or ill-health, between the ages of four and 14 years old.
The research is published in Proceedings of the Prehistoric Society.