Jordison was born at Mercy Hospital in Des Moines, Iowa on April 26, 1975. He grew up in a rural area outside of Waukee. He embraced music at an early age, attributing it to the influence of his parents; "they always sat me down in front of the radio, rather than the TV." He started his first band while in elementary school. He played guitar until receiving his first drum kit as a gift from his parents at age eight. At a young age, Jordison's parents divorced, he and his two younger sisters stayed with their mother. His mother remarried and set up a funeral parlor, where Jordison would occasionally help. Jordison has stated he felt a sudden responsibility to be the man of the house, and this responsibility turned him into a more mature person at a young age. 

Jordison did not enjoy his time at school, admitting, "I was really introverted and didn't have many friends." His grades suffered due to his focus on music. Despite being involved in multiple projects, he did not have his first serious band until he was 15; he formed Modifidious, in which he played drums, he later described them as "total speed-metal thrash". The band helped Jordison break new ground, playing for live crowds in support of local bands including Atomic Opera who featured Jim Root and Heads On The Wall, which featured Shawn Crahan. After a multitude of line-up changes, including the presence of Craig Jones and Josh Brainard — who would later appear in Slipknot — the band released two demos: Visceral and Mud Fuchia in 1993.

After leaving school he was hired by a local music store called Musicland. However, in March 1994, after a recommendation from a friend, he got a job at a Sinclair garage in Urbandale working the night shift. Jordison preferred the night shift, because it left his weekends free and he could hang out with his friends and listen to music while working. In early 1995, Modifidious disbanded due to a lack of interest, owed to the shift in interest from thrash metal to death metal in America. Following this Jordison joined a local band called The Rejects as a guitarist, with whom he only played a couple of shows. Jordison was also involved in a band called Anal Blast with Paul Gray; however, this was formed partly as a joke. Gray also attempted to recruit him for another band, Body Pit, but he declined the invitation to remain in The Rejects.

In September 1995, Paul Gray approached Jordison while he was working, offering him a position in a new project called The Pale Ones. Intrigued and at a point where he was "lost", Jordison attended rehearsals at Anders Colsefini's basement and immediately wanted to be part of this new band. Speaking of this moment he said, "I remember trying so hard not to smile, so I didn't look like I wanted to join, I remained poker-faced, but I thought they ruled." A lot of Slipknot's early development was discussed by band members while Jordison worked night shifts at Sinclair's garage. He is considered one of the most dedicated members of the band and is involved in most elements of the band including writing, mixing and production, and is reportedly "the first to arrive and the last to leave." Each member of Slipknot is assigned a number; Joey was assigned "#1". Although Jordison has always been closely involved in almost every aspect of the creation of Slipknot and the Murderdoll's music, including the mixing and production stages, he has only fully produced one album from either band, Slipknot's 2005 live album 9.0: Live. In August, 2008, Jordison broke his ankle and Slipknot had to cancel some of the England tour dates.