EMI would not disclose details of the settlement, which was reached last month.
An EMI spokesperson tells Billboard.com, "I can confirm that we have reached a mutually acceptable settlement and that we are not going to say anything more than that."
Apple Corps launched its latest legal action in December 2005 at the High Court in London and New York's Supreme Court, against EMI and Capitol, respectively.
The writ alleged unpaid royalties on Beatles albums based on an audit of sales between 1994 and 1999, a period which included the release of three "Anthology" compilations.
The latest settlement between Apple Corps and EMI follows a deal struck in February between Apple Corps and Apple Computer over the use of the Apple name.
That removed a major obstacle for Beatles tracks to appear on iTunes.
Earlier this month, EMI chief executive, Eric Nicoli, confirmed the major was working on making the Beatles catalog available for legal download for the first time.
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