The 45-year-old deleted his social media account shortly afterwards, the Daily Mail reports.
Reaction on Twitter has been divided, with some people utterly horrified and others defending Harmon's notoriously dark sense of humour which helped create hit comedy shows.
Many were left feeling sickened and questioning Harmon's mental health after seeing the video.
One Rick and Morty fan said the footage left her feeling "f***ing sick". While another added: "I just watched the Daryl video by Dan Harmon. Dan Harmon is a f***ing creep."
"F***ing disgusting, this guy got problems," someone else wrote.
Others suggested it could be the end of Harmon's career.
"Another one bites the dust, Dan Harmon. Looks like your career with Rick & Morty is over," one wrote.
Other fans explained that it was simply a running joke in poor taste.
"It was just an edgy, shock jock video that was trying to be so offensive that it became funny," one Twitter user wrote. "Whether or not you found it funny is subjective."
The 2009 video emerged just days after Guardians of the Galaxy director James Gunn was fired over decade-old offensive tweets.
Like Harmon, they appeared to joke about paedophilia and rape.
Among them was one where Gunn wrote: "I like when little boys touch me in my silly place."
In another he says: "The best thing about being raped is when you're done being raped and it's like 'whew this feels great, not being raped!'"
Nearly two dozen other tweets mainly in 2008 and 2009 were captured in screenshots before he deleted his account. The director and co-writer of the Marvel franchise, had been set to lead the third Guardians movie before Disney announced they were no longer working with him over the tweets.
Gunn had attempted to defend himself over the offensive tweets, explaining he'd made a career as a "provocateur" but had "developed as a person" and that his "days saying something just because it's shocking and trying to get a reaction are over."
"For the record, when I made these shocking jokes, I wasn't living them out. I know this is a weird statement to make, and seems obvious, but, still, here I am, saying it," he added.
The Guardians stars, Chris Pratt, Zoe Saldana and Dave Bautista have leaped to the director's defense since the scandal broke.
Even Family Guy has been forced to finally become more progressive in the wake of the #MeToo movement. Fans have seen the cartoon's creepy character Quagmire repeatedly rape women, from a bound and gagged underage cheerleader to a young, dead virgin.
Creator Seth MacFarlane says he is planning a Me Too episode for the character.
Meanwhile, Harmon has not commented on his Daryl video, to the surprise of his fans who are used to him doubling down on even his most offensive outbursts and comedy skits.
"Very weird that Harmon would delete social media after the Daryl video resurfacing. Isn't this the kinda shit he usually doubles down on," one Twitter user wrote.
The video, the first in a two-episode parody of Dexter was posted in June 2009 via Channel 101, a monthly short-film competition founded by Harmon and writing partner Rob Schrab.
It begins with a warning that the "controversial new pilot" is "a little groundbreaking for normal people to handle".
Harmon plays a child molester and therapist who uses his access to patients, to abuse and rape their children.
A graphic scene in the poorly produced short film shows Harmon pulling down his pants and simulating rape on a baby doll, whose head he turns to the side.
This is not the first time Harmon's "creepy" behavior has landed him in trouble.
In January this year, he used his HarmonTown podcast to confess his "filthy, creepy behavior" towards Community writer Megan Ganz who accused him of sexually harassing her when she worked on the show with him.
He admitted he'd been flirting with, pursuing and "creeping on my employee" and after being 'humiliated' by rejection he said "now I wanted to teach her a lesson".
He said he did "things that I would never ever ever have done if she had been male and if I had never had those feelings for her".
"I lied to myself the entire time about it, and I lost my job, I ruined my show, I betrayed the audience, I destroyed everything, and I damaged her internal compass. And I moved on."
Harmon finished up by saying: "So I just wanna say, in addition to obviously being sorry — but that's really not the important thing — I wanna say I did it by not thinking about it, and I got away with it by not thinking about it. And if she hadn't mentioned something on Twitter, I would've continued to not have to think about it, although I did walk around with my stomach in knots about it."
Ganz called his podcast "a masterclass in How to Apologise" and that she was able to forgive him.
Times reporters reached out to Harmon and Rick and Morty creators for comment.
