Speaking to Den of Geek, Millar said it was a year after they began before he and co-creator John Romita Jr saw any money from the project.
The pair were concerned about how successful the miniseries - published on Marvel's creator-owned Icon imprint - would be.
"But then the first issue outsold Spider-Man immediately - which was great - then we did five printings," he said.
"It took a while, but the money eventually came in, and we made more out of it than Civil War, and that was the biggest payday anyone at Marvel has had in years.
"Marvel probably s**t themselves, because people will start to realise, what's to stop their creators from doing creator-owned stuff, owning the movie and completely owning the comics?"
Civil War was the top-selling event comic of the last decade.
The Kick-Ass movie adaptation - directed by Matthew Vaughan (Stardust) - will premiere in April.