Everton, Wigan agree to compensation
Martinez has been the main target for the managerial vacancy at Goodson Park since David Moyes quit Everton for Manchester United last month.
The Toffees will now hold discussions with Martinez to finalize details of his contract on Merseyside.
Martinez informed Latics owner Whelan last week that he has decided to quit his post this summer following the club's relegation to the Championship.
The Spaniard is Wigan's most successful manager after winning the FA Cup in May with a 1-0 victory over big-spending Manchester City at Wembley.