Neville-Jones was called upon to stand down earlier this month after it was revealed she held shares in defence firm Qinetiq. She was reported to hold £50,000 in shares in the firm and last year earned £133,000 from the company as chairman.
Greg Dyke blamed Neville-Jones for helping to force him out as director-general following the Hutton Report.
However, a spokeswoman for the BBC has denied that the departure of Neville-Jones is linked to her involvement with Qinetiq.
Neville-Jones had been BBC's international governor since January 1998. Her departure will allow a new governor to be appointed in advance of the final phase of charter renewal decisions later next year.
As well as being linked to the former government-owned defence firm, Neville-Jones also had links to the intelligence community and was a former head of the Joint Intelligence Committee, a job until recently held by Sir John Scarlett, the new head of MI6.
While chairing the Joint Intelligence Committee, she advised the Prime Minister on foreign, defence and intelligence issues.
During the Dr David Kelly affair and ensuing Hutton Report she was highly critical of the BBC and for that earned the wrath of former BBC director-general Dyke. He accused her of leading the board of governors against him.
In a statement, Neville-Jones said that as the BBC approaches the final phase of decisions about its future, it was important for those involved to be established in post and ready to take responsibility for implementation of the outcome.
"I am due to retire from the board at what will be a crucial period of discussions and decisions about the BBC's future.
"I therefore believe the BBC would be better served to have a new international governor in place well in advance of December 2005 to provide continuity throughout the final phase of the charter renewal process."
BBC chairman Michael Grade said that Neville-Jones had been an outstanding champion of BBC World Service and BBC World and an effective chairman of the audit committee.
"We will miss Pauline's unwavering belief in the BBC," he said.
The calls for her to stand down came from backbench Labour MPs, including former defence minister Peter Kilfoyle and Llew Smith.
Smith said: "It is completely inappropriate that someone so senior in the BBC should be leading a firm making huge profits from the misery caused by the invasion of Iraq."
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