The Latics chairman confirmed to Sky Sports News on Wednesday evening that the highly-rated Spaniard would be staying at the DW Stadium.
Martinez held talks with Liverpool over the Anfield vacancy but Brendan Rodgers is now on course to be appointed, while Aston Villa have made Paul Lambert their No.1 target.
Whelan has claimed he was less concerned about the interest from the Midlands club, who failed with one bid to land Martinez 12 months ago, as he does not believe they are 'big enough' to lure him away from his current role.
The Wigan supremo said: "Roberto is staying at Wigan and, of course, I am absolutely delighted. He was never offered the job at Liverpool because he wasn't happy with the way the job was presented to him.
"He has had some talks with Villa, but he's not going to go there. Villa are a fantastic club with great fans, but I never thought they were big enough for him.
"I've said all along that I never thought he would end up there, and, fortunately for us, that's how it has turned out. If Roberto is to go anywhere, it will be to one of the top clubs in Europe. We're just so pleased that he's staying with us for another season."
Whelan and Martinez held talks on Wednesday and are now putting plans in place to ensure Wigan continue to compete in the Premier League.
The chairman added: "We've discussed a lot of things and it was a productive afternoon. He's got two years left on his current contract and we will be looking to extend that.
"We've also agreed to build up the academy and the training facilities.
"We want Roberto to be happy at Wigan and we'll be aiming to make sure we do everything to help him."
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