Former England great Lineker has attracted scrutiny from the broadcaster's critics for both his high pay package and his outspoken political views on social media that often criticised the ruling government.
The new contract will keep him at the corporation until 2025.
Addressing the latest report, Tim Davie said he expects stars to work at the BBC for lower pay than at competitors, but it is a "punchy" market. Zoe Ball, who hosts "The Zoe Ball Breakfast Show" on BBC Radio 2, was one of the highest earners across genders with $1.75 million.
Graham Norton is on at least £725,000 - a rise of around £115,000.
This is for his weekly show on Radio 2 and a range of TV programmes including his award-winning Friday night chat show and for his work presenting the BAFTA Awards.
Newsnight's Emily Maitlis' pay is on around £370,000 - with her pay bracket rising by around £110,000.
And while female stars continue to be outnumbered in the top ten list, the likes of Zoe, newsreader Fiona Bruce, journalist Vanessa Feltz and DJ Lauren Laverne have all been given pay rises.
Despite the job losses, however, presenters such as Zoe Ball saw her pay increase by £990,000 in the past year.
The number of senior managers earning over 150,000 pounds rose to over 100, the BBC's annual report showed, and BBC Chairman David Clementi said that the coronavirus crisis meant that the broadcaster had to save an extra 125 million pounds ($161.31 million). "She's delivering over eight million listeners", he said. "Of course we want to get value for everyone, but there will be particular instances where we've got exceptional talent where we'll make those investments".
Gary Lineker is to take a 23 per cent pay cut as he signs a new five year deal with the BBC.