Iain McMillan will leave the organisation towards the end of the year, a decision he said was made before the CBI registered for a No vote, triggering a spate of resignations from the body.
The organisation has endured a horrendous 10 days after it formally registered as a No supporter with the Electoral Commission.
Nearly 20 groups, including universities, broadcasters and private companies, either resigned or suspended their membership over fears of political impartiality.
The exodus prompted CBI director general John Cridland to announce that the CBI would de-register following what he described as an "honest mistake".
It can now be revealed that McMillan, the public face of the CBI north of the Border, will retire soon.
He told the Sunday Herald yesterday: "I made clear to the CBI two years ago that I did not want to go on to the age of 65 before retiring. It was agreed in January of this year that I would retire towards the end of this year".
McMillan, who turned 63 on Friday, was appointed director in 1995 and has executive responsibility for the body's operations in Scotland.
He is a respected business figure, but sources say he feels bruised by the events of the last two weeks.
It has been the CBI in London, rather than the Scottish organisation, that has taken the lead in publicly justifying the controversial decision.
Cridland's explanation of how the CBI reached the decision on registration is now under the microscope.
In a BBC interview, he said the decision was not "authorised" or "valid", adding that it had been made at a "junior level in London, not Scotland".
He said: "An official in our London office signed what he thought was a regulatory compliance necessary to deal with the CBI's expenditures on things like our events and our dinners.
"But, actually, of course, it opened a Pandora's box of unexpected consequences."
However, a CBI statement from eight days ago read: "The CBI is confident we have a mandate from the vast majority of our members on the question of Scottish independence. All CBI Scotland members have been regularly contacted by the CBI about the independence debate, with the opportunity to feedback their views.
"The final position was signed off by CBI Scotland Council - the membership decision-making body."
A spokesperson for the CBI said of the apparent conflict between the two statements: "The quotes about the final position being signed off by CBI Scotland referred to the CBI's independence position, and not the registration with the Electoral Commission."
It can be also be revealed that other organisations have been either considering their CBI membership or have left.
A spokesman for Business Stream, which supplies water to private-sector clients, gave a statement to
this newspaper last week before the CBI decided to de-register:
"We note the decision which CBI Scotland has taken regarding the upcoming referendum and as a result have decided to resign our membership. Business Stream is strictly impartial regarding the issue of independence, which is a matter for the Scottish electorate."
A spokesman for the Institute of Chartered Accountants of Scotland said: "We are currently reflecting on the developments at the CBI and will be discussing this further later this week".
Callum Spreng, managing director of PR firm Spreng & Co, said his firm's CBI membership would be considered "at renewal".
The CBI is also declining to answer questions about the composition of its Scotland council. It had a copy of its 2011 council membership online recently, but refused to provide an updated list on the grounds of "data protection". After the Sunday Herald told the CBI about the existence of the 2011 list, it disappeared from the website.
Tony Banks, the chairman of the pro-independence Business for Scotland group, said: "The news that Mr McMillan will soon be departing from CBI Scotland comes as no surprise. His silence during the last week speaks volumes. Mr McMillan's retirement may suggest to some people an element of scapegoating to distract from the central CBI figure, director general John Cridland. His own position now looks untenable."
Green MSP Patrick Harvie said: "The CBI is clearly not just a business network - it's a free-market, right-wing lobbying group whose Scottish boss recently described inequality as an 'abstract' term. Given the recent exodus of members, the question must now be why public bodies and neutral broadcasters ever joined such a lobby group."