That means he could earn less than Zoe Ball next year.
Mr Nolan's pay is for presenting the Nolan Show on BBC Radio Ulster, The Stephen Nolan Show on BBC Radio 5 Live and Nolan Live on BBC One Northern Ireland.
Lineker said: "I love working with the BBC, and am very proud to continue to be a part of their outstanding football team".
"His published salary each year may vary, depending on when payments for work completed are actually made".
On top of Lineker's pay cut, the BBC's report has revealed significant pay increases for many high profile women in the corporation.
The BBC Annual Report confirmed that Zoe's pay soared from £370,000 in 2019 to a minimum of £1.36 million.
In fact, 76 of the BBC's presenters now earn more than UK Prime Minister Boris Johnson, whose annual salary is £150,000.
"The focus today will rightly be on some of the huge salaries paid to individuals. The BBC is extremely pleased to have him leading our coverage so exceptionally for another five years".
DUP MP Gregory Campbell said the publication of the list of top earners at the BBC will be viewed by those over 75 losing their free TV licences as a demonstration of where the corporation's priorities lie.
Gary Lineker has signed a new, five-year contract with the BBC.
A £65,000 pay rise for Stephen Nolan has been defended by the BBC despite it coming as the broadcaster is under pressure to slash costs. BBC Studios production was the U.K.'s most commissioned creator of new content in 2019, with 77 new commissions from the BBC and third parties.
Overall, BBC Studios reported a strong 2019/2020 financial year in its results on Tuesday, which covered the year up to March 30.
However the BBC is facing increasing competition from subscription services, with 13m households in the United Kingdom paying for Netflix for example.
The BBC drama Normal People, for example, was requested 55m times on BBC iPlayer from early April until the end of July. Season five of Line of Duty had an audience of 13.2 million for the first episode.
91% of adults and 81% of children use BBC radio, TV or online every week, making it by far the most-used media organisation in the UK. BBC iPlayer had a record 4.8 billion requests to stream programs in 2019/20.
BBC Chairman David Clementi commented: "This annual report tells the story of a BBC that remains of huge value at home and overseas, but is not without considerable challenges".