It ends a troubled period for that club and their Scottish coach.
Kean has been a much-derided figure at Ewood Park for the duration of his near two-year spell in charge, with the low point being relegation from the Barclays Premier League in May.
But despite poor results on the pitch, Kean retained the backing of the club's owners, Venky's, much to the fury of supporters who regularly protested against him.
The tide seemed to have turned for the 44-year-old this season, on the pitch at least, as Blackburn made a positive start to the campaign; Rovers sit third in the npower Championship table ahead of today's trip to Charlton Athletic.
Fan unrest has continued, though, and in a statement issued through his lawyers, Kean last night said: "For reasons that I cannot discuss on legal advice, it is with deep regret, given my hard work and service for the club for a number of years, that I have been forced to resign as manager of Blackburn Rovers Football Club with immediate effect, due to my position as team manager becoming untenable.
"I wish to thank all the players and coaching staff for their great support and the majority of the fans, who now see their club heading toward automatic promotion back to the Premiership. I wish the club all the very best for the future."
There was no sign of Kean's decision to step down on the club's official website, with the lead story there one of him talking of a "positive week".
When contacted, Derek Shaw, the managing director said: "I have been travelling down to London and this is the first I have heard of it."
Kean was appointed as manager of Blackburn in December 2010, replacing Sam Allardyce who was relieved of his duties despite saving the club from relegation the previous season.
Kean's contract was upgraded a month later and, although he kept them up that season, it was clear he was not a terrace favourite.
As Rovers struggled at the start of last season, the calls for Kean to stand down became stronger but despite that, he was again given an improved deal by Venky's in November.
Regular protests reached their most vicious when Blackburn lost a home fixture against their relegation rivals Bolton Wanderers, but Venky's remained nerveless, standing by their man even when the club's seemingly inevitable relegation was confirmed when they drew at Wigan Athletic in May.
Even the most loyal fans of Blackburn expected Kean might be relieved of his duties over the summer, but the faith remained in the boardroom, despite disparaging public comments from director of football Shebby Singh, who had to apologise for stating Kean would be sacked if he lost three games in a row.
Kean was heavily backed in the transfer market, signing Huddersfield Town's Jordan Rhodes for £8m, but despite only losing their first league game of the season last Friday, he remained under heavy pressure.
Singh did little to douse the fires this week when he said the situation was getting worse "day by day", with those comments coming three days before Kean's decision to stand down.
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