Kermit the Frog guest co-hosted the show for a week, and later appeared as a guest, in the fall of 2003.
In April 2005, Grover made a rare late-night appearance, promoting the Happy Healthy Monsters DVD and the 36th season of Sesame Street. On May 13, 2005, Fozzie Bear was a guest (along with Ozzy Osbourne) promoting The Muppets' Wizard of Oz. He also brought along Rizzo the Rat and performed stand-up for the audience.
On November 4th, 2009, Big Bird (Caroll Spinney) appeared to promote Sesame Street's 40th Season (other guests included Joshua Jackson). Big Bird doesn't remember Laura Bush appearing on the show (in Episode 4032). That's because Big Bird was being performed by Matt Vogel in that segment. Oscar the Grouch made a surprise appearance before the show in his garbage can on Jimmy's desk as a teaser for the show.
After the 2012 Academy Awards, Kimmel's special episode started with a pre-taped skit of Billy Crystal leaving the Hollywood and Highland Theatre, and making a shady deal for an Oscar. It isn't the Oscar that Kimmel was hoping to purchase.
- September 29 - October 3, 2003: Kermit the Frog guest co-hosts
- November 28, 2003: Kermit the Frog
- October 3, 2003: Kermit the Frog with Christina Cindrich
- April 4, 2005: Grover
- May 13, 2005: Fozzie Bear along with Rizzo the Rat
- November 4, 2009: Oscar the Grouch (cold open only), Big Bird
- February 18, 2011: Oscar The Grouch (prerecorded, "Name That Oscar Winner" segment)
- November 14, 2011: Miss Piggy, to promote The Muppets
- February 26, 2012: Oscar the Grouch (in conjunction with the Academy Awards)
- March 21, 2012: Dr. Teeth and the Electric Mayhem perform "Can You Picture That?" with Travis Barker
- March 3, 2014: Gonzo appeared in promotion of Muppets Most Wanted
- March 4, 2014: Sam the Eagle appeared with Guillermo Rodriguez in a comedy segment
- February 12, 2015: Cookie Monster appeared in promotion with The Cookie Thief
- September 21, 2015: Kermit and Miss Piggy promote The Muppets in an interview with Kimmel , and The Swedish Chef prepares chicken in the green room.
- In a 2005 segment in which Kimmel visits the set of Lost, the often rumored "monster" which terrorizes the island is revealed to be none other than (a giant) Cookie Monster who asks, "Anybody have cookie?"
- The June 27, 2008 broadcast included a "Come and Play" Edition of their recurring Unnecessary Censorship segment. The montage unnecessarily censored clips from Sesame Street.
- A 2009 sketch parodying the arrest of Bernie Madoff featured Cookie Monster explaining a Ponzi scheme by bilking Ernie out of his cookies.
- Two 2009 sketches satirized the trailer of The Twilight Saga: New Moon: one featuring The Count as a new villain, and another featuring werewolf Jacob transforming into Mr. Snuffleupagus.
- On the October 30, 2009 Halloween episode, Kimmel and his staff spent the entire episode dressed as Sesame Street characters. Kimmel dressed as Big Bird, his band, Cleto and the Cletones, included Ernie, Bert, Super Grover, Cookie Monster, Zoe, and the Count, Dicky Barrett the announcer dressed as Oscar, and security guard Guillermo was dressed as Elmo. Also on the episode, footage of Cookie Monster was re-dubbed in a satire of Celebrity Rehab.
- On the January 15, 2010 episode, Kimmel talks about how Sesame Street characters are appearing in video games. This leads to a scene from a videogame of Grand Theft Auto and the title of the game is called, "Grand Theft Sesame Street.
- On the January 29, 2010 episode, Kimmel talks about how Jersey Shore' is so popular that the characters are appearing in other TV shows. This leads to a hand puppet of Cookie Monster singing about Snookie to the tune of "C is for Cookie."
- On the September 23, 2010 episode, Kimmel talks about Sesame Street's controversial Katy Perry video and replies while moms are complaining about Kate Perry's outfit, they never notice that most of the Muppets are naked. He also says that Sesame Street isn't innocent as it use to be and was shock when he saw a commercial for it's new DVD. This lead to a commercial of a show combined of Jersey Shore and Sesame Street called Sesame Shore.
- On the March 3, 2014 episode, Kimmel aired a short film called David After Dentist Double Rainbow Oh My God! in 3D, parodying a variety of viral YouTube clips. While drugged out on dentistry drugs, David (Joseph Gordon-Levitt), a fairy (Catherine Zeta Jones), and a flying hippie (Seth Rogen) sing "The Rainbow Connection". Samuel L. Jackson also stars.
- On the February 18, 2016 episode, Nikolaj Coster-Waldau tells Kimmel that he have always dreamed of being Big Bird. Kimmel then starts to list his favorites Ernie, Oscar the Grouch and Cookie Monster and conclude that his absolute favorite had to be Cookie Monster. Kimmel also asks Nikolaj if he have been on Sesame Street. A short while later Kimmel talks about the U.S presidential campaign he says "we don't see these people as Muppets, we see them as our leaders", referring to the presidential candidates.