The Guardians of the Galaxy director came under fire for the two-year-old Facebook entry, which the Lady Geek blog uncovered and declared "sexist" and "homophobic".
The post, which listed the superheroes - including Batwoman, Emma Frost and Gambit - that Gunn would have sex with, has since been removed.
"A couple of years ago I wrote a blog that was meant to be satirical and funny," he wrote on his Facebook page.
"In rereading it over the past day I don't think it's funny. The attempted humour in the blog does not represent my actual feelings. However, I can see where statements were poorly worded and offensive to many. I'm sorry and regret making them at all.
"People who are familiar with me as evidenced by my Facebook page and other mediums know that I'm an outspoken proponent for the rights of the gay and lesbian community, women and anyone who feels disenfranchised, and it kills me that some other outsider like myself, despite his or her gender or sexuality, might feel hurt or attacked by something I said.
"We're all in the same camp, and I want to do my best to make this world a better place for all of us. I'm learning all the time. I promise to be more careful with my words in the future. And I will do my best to be funnier as well. Much love to all - James."
The Super and Slither director has signed on for Marvel Studios 'Phase Two' cosmic ensemble movie, which is currently in the casting stage.
Guardians of the Galaxy is scheduled to debut on August 1, 2014.