The Silkmen have received an undisclosed transfer fee and Whitehead, who has signed a two-and-a-half year deal at the DW Stadium, will return to the Moss Rose on loan for the rest of the season.
Whitehead has been a key figure for the Silkmen after his arrival last summer.
The former Stockport County and West Ham United man originally came in on trial after leaving Accrington Stanley last term and quickly caught the eye.
Several impressive displays in pre-season saw him sign a deal with the Silkmen and he has so far made twenty-seven appearances in all competitions for Macclesfield. He also has found the back of the net on five occasions and assisted two more goals for John Askey's side.
Whitehead will now look to continue his development with Macc for the rest of the season, before linking up with his new side in the summer.
Wigan manager Gary Caldwell says Whitehead is a player for the future: “Like our new signing from Torquay United, Dan Lavercombe, he’s one we have watched at length and identified as having the potential to play at a higher level.
“Every club is on the lookout for fresh talent and it is a case of acting fast and looking to the future with these signings.
“Now that everything is over the line, like Dan, he will combine his training here and with playing for his former club, as he gains more first team experience and we also get to know him.”