The Match Of The Day host is the biggest earner, taking home between £1.75 million and £1,759,999.
He replaces Chris Evans at the top, who is shown to be earning between £1.6 million and £1,669,999 for his Radio 2 Breakfast show.
Last year’s accounts showed the Radio 2 Breakfast DJ took home up to £2,249,999 in the 12 months to April 2017 and his salary has been reduced since stepping down from Top Gear.
The top 10 published this year is made up of men, with Lineker and Evans followed by Radio 2 DJ Graham Norton, on up to £609,999 - not including payments for his TV chat show.
The other big earners are also men - broadcasters Steve Wright, Huw Edwards, Jeremy Vine, Alan Shearer, Nicky Campbell, Nick Grimshaw and Stephen Nolan.
The BBC argues that the list does not reflect the true balance of payments to men and women as salaries through BBC Studios, which is not funded by the licence fee and became a commercial entity, are not revealed.
If included, they would feature payments to Claudia Winkleman for Strictly Come Dancing, Alex Jones for The One Show and Fiona Bruce for Antiques Roadshow.
It also says that changes to pay packets in recent months are also not reflected as the list is compiled from salaries up to April this year.
There are women on the list who did not appear last year.
Mary Berry’s salary is published this year, showing the former Great British Bake Off judge earns between £190,000 to £199,999 “for a range of programmes and series”.
Women who are on the list of stars earning more than £150,000 this year and appear to have received pay rises include Newsnight’s Emily Maitlis.
Maitlis, who was absent last year despite co-host Evan Davis appearing, took home between £220,000 and £229,999.
Woman’s Hour host Jane Garvey, who has been outspoken in her criticism of the gender pay pay, is another new name and was paid between £150,000 and £159,000 for work which also includes programmes on 5 Live and episodes of Fortunately.
Other female stars to appear this year include Newsbeat’s Tina Daheley, who was paid between £150,000 and £159,000, which also includes cover for BBC Breakfast and Victoria Derbyshire.
This year’s report also features 5 Live Breakfast’s Rachel Burden, Europe editor Katya Adler and Scotland Editor and Sunday Politics journalist Sarah Smith.
Over the last 12 months, the BBC has announced pay cuts for some of its male stars, including broadcasters John Humphrys, who had been paid more than £600,000, Vine, who was on more than £700,000, and Edwards, who was on more than £550,000.
It was disclosed that Today host Humphrys’s salary would drop to below £300,000, Radio 5 Live star Campbell’s to below £350,000 and newsreader Edwards’s to below £500,000 - less than what has been published because the report only reflects the past financial year.
Last year, BBC stars were able to see what their colleagues were paid when the corporation published salaries for 96 people for the first time.
It catapulted the broadcaster into turmoil, with respected China editor Carrie Gracie resigning over unequal pay.
On Wednesday, salaries were revealed in bands of £10,000 rather than last year’s £50,000, after discussions with the Government over transparency.
The BBC also published the detail of which programmes its stars have worked on, which it hopes “will help ensure that more informed comparisons can be made”, a BBC source said.
The BBC recently published figures showing it had reduced its gender pay gap by nearly a fifth.
A BBC source said: “The BBC has come a long way in a short period of time. The job is not done yet, but we are making good progress.”
Speaking at a press conference, BBC Director-General Tony Hall said: “It’s not a 60/40 gender pay gap, I’m saying that of the figures of men versus women, who are now paid over £150,000 a year, you’ve got 60 per cent men and 40 per cent women.
“I’m focusing on that because these things take time and to begin to change the dynamics of what people are paid takes time, it’s important we focus on where we are now right here which is why 60/40 matters ... but I’ve made it absolutely clear that’s not good enough and I want to get to 50/50, and that will mean changes in the range of what people are paid right across (the organisation)”.
Lord Hall continued: “What I’m saying to you is am I satisfied with that, of course I’m not. We are making progress and you must understand that.
“We’re trying to get a balanced range of men and women and their pay right cross the organisation, I am concentrating on what is a huge change, which is going from 25 per cent of women to 40 per cent of women being in the top, over £150,000 pay... These things take time.”
The top 12 highest-paid stars listed in the annual report (April 2018 - March 2017) are:
Gary Lineker - £1,750,000 - £1,759,999
Chris Evans - £1,660,000 - £1,669,999
Graham Norton - £600,000 - £609,999
Steve Wright - £550,000 £559,999
Huw Edwards - £520,000 - £529,999
Jeremy Vine £440,000 - £449,999
Alan Shearer £410,000 - £419,999
Nicky Campbell £410,000 - £419,999
Nick Grimshaw £400,000 - £409,999
Stephen Nolan £400,000 - £409,999
John Humphrys £400,000 -£409,999
Andrew Marr £400,000 - £409,999