Wilkes is known as the founder and only remaining original member of the Legendary Shack Shakers, a rockabilly and blues band he formed in Murray, Kentucky, in the mid-1990s. Before forming the band, Wilkes was a performer on the paddle-wheel boat, Paducah Jubilee. He also played harmonica for the neo-vaudeville act "Popularity Showboat". His first live, professional performance was with the group at the Kentucky State Penitentiary.[5]
Regarding the Shack Shaker's "southern gothic" lyricism, Billboard Magazine said "[Wilkes writes] mind-blowing lyrics rife with Biblical references and ruminations of life, death, sin and redemption."[6]
His contributions to the visual arts include many illustrations, comic strips, and sideshow banners. His satirical "Head Cheese" strip ran in the Nashville RAGE/Metromix weekly from 2005 to 2008. Other illustrative works by Wilkes have been published in Juxtapoz, Snicker, Mineshaft, ALARM Magazine, and TopShelfComix.com.[8] Wilkes illustrated the book Spookiest Stories Ever for the University Press of Kentucky, released in 2010.[9]
In October 2013, The History Press published Wilkes' book Barn Dances and Jamborees Across Kentucky, a history of traditional music get-togethers in the Bluegrass State.[10]
In 2006, Wilkes, began work on a documentary film titled Seven Signs, that explored "music, myth, and the American South".[11] The film premiered on December 30, 2007, at the Belcourt Theatre in Nashville, Tennessee and debuted in the UK at London's prestigious Raindance Film Festival.[12] In early 2009, Wilkes formed The Dirt Daubers, an old-time roots-influenced side project with his now ex-wife, Jessica, and "Slow" Layne Hendrickson. The band's self-titled debut was released in October 2009. They were later referred to as JD Wilkes and the Dirt Daubers.
Occasionally, Wilkes and the Shack Shakers appear in the Danish theatrical production F.U.B.A.R., a production of Copenhagen's Mute Comp Theatre. The play, which tackles the subject of illegal gun trade around the globe, features a speaking part by Wilkes. He also reprised his "gothic preacher" character (developed for Shooter Jennings' The Real Me video) when he acted as the presenter at the 2013 Addy Awards in Cincinnati, Ohio.
In May 2014, Wilkes was selected by mayor Gayle Kaler to represent his home city of Paducah, Kentucky, in a cultural exchange with The Lord Mayor of Dublin, Ireland. Wilkes was met by author/actor/playwright and deputy Lord Mayor Gerard Mannix Flynn at the Mansion House in Dublin, where the two exchanged gifts as part of a UNESCO-sponsored reception.
In March 2017, independent publisher Two-Dollar Radio released Wilkes's novel The Vine That Ate The South, a book praised by NPR as "undeniably one of the smartest, most original Southern Gothic novels to come along in years".[13][14] "Wilkes’ ability to spin a story and craft language that's as inventive and clever as the book's plot combine to create something special that's a bit of a contradiction itself—a book that feels both classic and new, mythic and modern".[15]