Homestar Runner (H*R) is a web-based Flash cartoon series created by "The Brothers Chaps," Mike and Matt Chapman. The series revolves around the title character Homestar Runner, his friends, and their would-be nemesis Strong Bad.
The series makes frequent references to the Muppets, the most obvious of which are the "Puppet Stuff" shorts, in which several H*R characters appear in puppet form. The "Vs." series of Puppet Stuff shorts, which feature Homestar and Strong Bad alongside Little Girl (or Other Little Girl), are reminiscent of the Sesame Street segments in which a Muppet character interacts with a young child. The most recent of these shorts, which pitted Homestar against a baby (or, Very Very Little Girl) may very well be a reference to Elmo asking a baby questions in Elmo's World.
- "Halloween Potion-Ma-Jig" - The 2005 Halloween cartoon features Marzipan dressed as Beaker. When Marzipan imitates Beaker's voice, The Cheat, who speaks in a similar high-pitched sqeak, appears to understand her.
- "Strong Bad Email #44 - lures & jigs," in which Strong Bad and Coach Z go fishing in a scene similar to a Sesame Street skit involving Bert and Ernie on a fishing trip.
- "Teen Girl Squad" issue 7, in which the normal teenage girl characters appear as toddlers called the Teeny Tiny Girl Squad. The Brothers Chaps, the creators of H* R, have said this is a direct homage to Muppet Babies.
- "Strong Bad Email #140 - highschool," in which several regular H* R characters appear as (in Strong Bad's words) "melon-headed babies with gigantic eyes and enormous imaginations." When the babies imagine things, black-and-white photographic images appear behind their cartoon forms, referencing Muppet Babies' frequent use of old film footage. Homestar himself takes the role of Nanny, wearing red and white striped bloomers instead of green and white striped stockings.
- "Strong Bad Email #110 - for kids," in which the character Homsar hosts a children's show called "Whaddaya Know, Haddi-Man?", which is very similar to Sesame Street.
- "Jibblies 2" - The 2007 Halloween cartoon features Homsar as The Typewriter from Sesame Street.
- "Strong Bad's Cool Game For Attractive People Episode 1: Homestar Ruiner" (2008 Wii and PC game): after collecting four trophies for in-game achievements, Strong Bad imitates The Count: "Four! Four outrageous trophies! Ah ah ah!" Also, at a party, Strong Bad speaks to Coach Z in faux Swedish, ending with the Swedish Chef's famous "bork bork bork."
- "The Animated Adventures of Puppet Homestar" - The RSS Feed description for the cartoon mentions the Muppets.
- A September 23rd, 2018 tweet from @StrongBadActual features part of script for the unfinished episode "Dangeresque: Roomisode 2". A line from Talk Trashcan reads "Hands up, Oscar! We know what REALLY happened to Mr. Hooper!" 
- In the online video, "Beaker's Ballad", when Beaker's set ignites, a comment appears that reads "BURNINATION!", a reference to Trogdor the Burninator.