The Justice League design pays homage to José Luis García-López's classic Justice League of America illustration.
The T-shirt will be available to pre-order in January for its release on April 11.
"It's an honour to have Jim Lee design 2012's FCBD Commemorative T-shirt," said Free Comic Book Day spokesperson Leslie Bowser.
"Jim's artwork featuring the Justice League from DC Comics: The New 52 will certainly entice a lot of current fans. And it's all for a good cause, as all proceeds go to our marketing efforts to spread the word about FCBD to new customers."
Previous FCBD T-shirt have featured designs by Sergio Aragones and Darwyn Cooke.
Lee is currently illustrating DC's flagship Justice League title alongside writer Geoff Johns.
Free Comic Book Day allows publishers to promote their titles with free editions of their comics.
It is held on the first Saturday of May. Free Comic Book Day 2012 will fall on May 5.
> Free Comic Book Day 2012 Gold Titles unveiled
> Free Comic Book Day 2012 Silver Titles unveiled