After 48 hours of constant pain, Fiennes sent up two distress flares to indicate he could not continue his 1,800-mile, 110-day trek across the South Pole.
As a rescue plane picked him up from his camp, his wife Lady Fiennes said the news was "bitterly disappointing" after all the hard work he had put in.
Speaking from their Devon home, she said: "This was the last thing we expected to happen. He has had kidney stones before and was therefore taking medication to prevent them. The maddening thing is that once the stones come out he will be okay again - he is very fit."
She added: "If the stone cannot get out and needs surgical removal, it could cause infection and kidney failure. He left it as long as he possibly could."
Lady Fiennes said she had no idea whether this would be her husband's last attempt to walk across Antarctica, but would be speaking to him later today.
The distress flares were spotted by his back-up team earlier yesterday. He was nearly a quarter of the way into the expedition and had otherwise been making good progress.
He reportedly radioed his base camp to say simply: "I need help. Get me out."
After he was picked up by the plane, a spokesman for his sponsors said Sir Ranulph was " feeling ill" and was being taken for medical treatment.
Dr Mike Stroud, the expedition's medical adviser who failed in an earlier attempt to complete the feat along with Sir Ranulph in 1992, said he was "very, very disappointed" for the explorer.
Dr Stroud told ITN that kidney stones could be extremely debilitating. "It's meant to be the worst pain you can get and it makes you feel very sick and ill - and alone in a tent and out in Antarctica, it must have been miserable."
Sir Ranulph had hoped his mission would raise more than pounds 1m for the breast cancer charity Breakthrough.
He was competing against international explorers who set off at a similar time and he was understood to be trailing slightly behind his main rival, the Norwegian Borge Ousland, who is 20 years his junior.
The adventurer, who suffered from kidney stones six years ago during an unsuccessful attempt to cross the North Pole, was forced to hole up inside his tent around 450 miles from the start line when the pain became too much for him to continue dragging his heavy sledge across the ice.
However, it emerged later that his expedition was not completely in vain. James Dyson, sponsor of the expedition, said his company would still donate pounds 1.44m to the charity in recognition of Sir Ranulph's efforts.Reuse content