Ferguson has not spoken to the organization's television or radio outlets about United since 2004 following the broadcast of a TV documentary containing allegations about his son Jason.
The 69-year-old Scot had said he would not speak to the BBC again until an apology was made for the comments about his son and the only interviews Ferguson has given to the national broadcaster have been for tributes to figures such as Sir Bobby Charlton and Ryan Giggs.
That left the BBC forced to make do with pre and post-match interviews with Ferguson's assistant Mike Phelan and United players instead.
However, earlier this year the BBC expressed their disappointment to the Premier League when Ferguson refused to speak to any media outlets after a defeat at Liverpool.
They stopped short of an official complaint but the Premier League, who can fine managers for refusing interviews, orchestrated a meeting in an attempt to end Ferguson's boycott.
Interviews with Ferguson will now return to Match of the Day, the BBC's flagship football highlights programme.
A joint statement released by United and the BBC on Thursday read: "Sir Alex Ferguson and the BBC have decided to put behind them the difficulties which led to Sir Alex feeling unable to appear on BBC programmes.
"This follows a meeting between Sir Alex and the BBC's director general, Mark Thompson, and BBC North director Peter Salmon, and the issues have been resolved to the satisfaction of both parties.
"Sir Alex will now make himself available to the BBC for Match of the Day, Radio 5 Live and other outlets as agreed."
Alex Ferguson ends BBC boycott
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