Charles' missive was written to interior designer and good friend of both Charles and Diana, Dudley Poplak.
The letter is dated December 11 1992 - just two days after Prime Minister John Major announced the formal separation of the Prince of Wales and Princess Diana.
It is written on H.M. Yacht Brittania-crested paper and concludes by thanking Mr Poplak for being "hugely reassuring and comforting", and sending "countless good wishes".
Among the four other letters going to auction is another from the Prince of Wales to his friend and landscape consultant Vernon Russell-Smith.
This letter is dated November 10 1988 and defends the Prince's strong opinions against modern architecture - which remain controversial to this day.
This letter refers to a media frenzy Prince Charles had created after the BBC had aired the 75-minute documentary A Vision of Britain on October 28 1988 - giving full voice to the Prince's strong criticisms of modern architectural projects.
In the typed letter to Mr Russell-Smith, Charles argued, "I was trying to strike a blow for the 'ordinary bloke's' point of view."
"I hope it will encourage some people to pluck up courage to call the experts' bluff!" he wrote.
He added: "Perhaps in 30 or 40 years time I will be viewed as someone who got it all wrong and my memory will be reviled."
Chris Albury, auctioneer and senior valuer at Dominic Winter Auctioneers, said, "It is interesting to read his firm belief that he was giving voice to the 'ordinary bloke' while realising history will judge him on his views later.
"It is 30 years since he wrote this letter and his views continue to draw praise and outrage in equal measure."
Referring to the letter to Dudley Poplak, Mr Albury added: "Even more unusual is to have a very personal and revealing letter from Prince Charles candidly expressing his pain and frustrations, too."
Dominic Winter Auctioneers will also auction off a pair of white leather peep-toe shoes, believed to have been worn by Princess Diana at the age of about 19, and a letter written by the late Princess, also addressed to Dudley Poplak.
Written on Kensington Palace-crested paper in February 1992 - also against the backdrop of a failing marriage - Diana thanks Mr Poplak for sending her some philosophical readings.
She writes, "I have been fascinated by the contents of the Daily Meditations, as for a couple of years now I've followed the French philosopher Omraam Mikhael Aivanhov's way of thinking.
"You are marvellous, Dudley, the way you've kindly sent me all these things to read - they do interest me enormously."
Omraam Mikhael Aivanhov was a Bulgarian philosopher and mystic who taught that to achieve a better life one must have a high ideal.
Mr Albury said, "We've seen a good number of letters from Princess Diana over the years, including letters like this that have added poignancy and give insights into her personal life and character.
"Emotionally charged letters like this, which reveal her genuine interest in new age philosophy against the backdrop of a failing marriage, are very collectable."
The letter from Diana is expected to fetch between £500 ($897) and £800 ($1436) at the auction in Cirencester, Glos.
Meanwhile, Charles' letters to Dudley Poplak and Vernon Russell-Smith each carry an estimate of £300 to £400, while Diana's shoes carry a 'modest' estimate of £300 to £500.
Dominic Winter Auctioneers will also auction a further two letters from Prince Charles to Vernon-Russell Smith, both concerning plants that have or could be planted in the Prince's garden.
These both carry an estimate of £200 to £300 each.
