The president is unlikely to complain about the comic caper as he was a collector of the Spider-Man comics as a child.
Joe Quesada, editor-in-chief at Marvel, said: "How great is that? The commander in chief to be is actually a nerd in chief."
The special edition features Obama on the cover, with Spider-Man in the background saying "Hey, if you get to be on my cover, can I be on the dollar bill?".
It will be distributed as a bonus with Spider-Man edition #583, on sale on January 14 at $3.99, six days ahead of the real-life inauguration.
In the story Spider-Man's everyday alter-ego Peter Parker spots two identical Obamas at the ceremony, which is due to take place on January 20, and works out that one of his arch-enemies is up to no good.
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