"Yoda" was played at the end of every show for the tours promoting Yankovic's albums Dare to Be Stupid, Off The Deep End, Alapalooza, Bad Hair Day, Running with Scissors, Poodle Hat, Alpocalypse, and Mandatory Fun. He also occasionally used it to end shows of the Ridiculously Self-Indulgent, Ill-Advised Vanity Tour of 2018, and it is included in the "Unplugged Medley" which ended concerts of the Unfortunate Return of the Ridiculously Self-Indulgent, Ill-Advised Vanity Tour. Starting with the 1999 Touring with Scissors shows, the song has been preceded by that album's Star Wars–themed single, "The Saga Begins". For the Straight Outta Lynwood tour, the band moved both songs to the middle of the set, and performed "Albuquerque" as their finale. Beginning in June 2010, "Yoda" has again been the final encore. Unlike the album version of "Yoda", which uses the same instrumentation as "Lola", Yankovic adds accordion accompaniment in live performances; this can be seen on the video releases "Weird Al" Yankovic Live! and "Weird Al" Yankovic Live! – The Alpocalypse Tour.
Since 1992, an a cappella chant (often referred to as the "Yoda chant"), originally performed during the bridge of "Another One Rides the Bus" in 1991 during the Dr. Demento 20th Anniversary Show, has been included in live performances, and is considered a staple of Yankovic's shows. Midway through "Yoda", the band slowly ceases playing and goes into the chant, which Yankovic wrote himself. Originally, the chant consisted mainly of mnemonic syllables accompanied by synchronized movements from the band. Over the years, the chant has grown to include, among other things, pieces from "Grim Grinning Ghosts" (the theme to Disneyland attraction The Haunted Mansion), phrases from The Trashmen's "Surfin' Bird" and "Frère Jacques", and elements of the "Hawaiian War Chant" and the "Aussie Aussie Aussie, Oi Oi Oi" chant. On the Mandatory Fun Tour in 2015, a piece of the "four-way-crimp" from The Mighty Boosh was also added, on the Unfortunate Return of the Ridiculously Self-Indulgent, Ill-Advised Vanity Tour in 2022, an excerpt of "The Lion Sleeps Tonight" was added to the chant in addition to a Balinese kecak. Most recently in 2025, on his Bigger and Weirder Tour, he added the beginning of “Hooked on a Feeling”.
In 2015, as part of Comedy Central's Night of Too Many Stars, a benefit for New York Collaborates for Autism, Yankovic performed the song with 13-year-old Jodi DiPiazza, a noted autistic pianist.
