Pavitt grew up in Illinois, attending the same high school as future Soundgarden guitarist Kim Thayil. Unhappy attending Blackburn College in his home state, he followed Thayil, who had transferred to the progressive Evergreen State College in Olympia Washington. At the wildly liberal college, Pavitt immersed himself in the local scene, working at the campus radio station, KAOS, and as an intern at OP magazine, while claiming to earn a degree in punk rock from the college. Becoming interested in local scenes outside of Olympia, Pavitt put together a fanzine, Subterranean Pop (for which he got school credit), designed to highlight local scenes around the country through a cassette-only release. The release featured Jad Fair and Jason & the Scorchers, among others, and proved to be Pavitt's first foray into running a label.

After graduating from Evergreen, Pavitt moved to Seattle, where he wrote a column for the city's local music paper, The Rocket, as well as DJ-ing a local music show at KCMU. Several bad jobs later, he wound up at Muzac, the company known for supplying elevator and department store music, where he secured employment for several of his friends, including Mark Arm of Mudhoney and Tad Doyle of Tad. At the muzac warehouse, the ethos for the Seattle scene started to take shape and, borrowing money from his father, Pavitt distributed another album. In 1986, Sub Pop 100 was released and included a collection of bands from scenes around the country such as Sonic Youth (New York) and Steve Albini (Chicago), as well as several local bands like the U-men, Green River, and the Wipers. Pavitt's idea of forming an independent label to empower local bands was starting to take shape, and later the same year, with local promoter Jonathan Poneman enlisted as co-partner, Sub Pop officially released its first album, Green River's Dry as a Bone EP. Soundgarden's Screaming Life/Fopp soon followed, and with Charles Peterson's blurry black-and-white cover photos and Jack Endino's raw production, the Seattle look and sound took shape.

After several more releases from local groups such as Tad and Mudhoney, Pavitt and Poneman signed the act that would change their future, Nirvana. Releasing the single "Love Buzz," the label sent the group on a tour of England, but Sub Pop's chronic financial troubles proved for a difficult tour and the group quickly returned to record their first album, Bleach. As a last ditch effort, Pavitt flew a young music writer from the British magazine Melody Maker to Seattle in hopes of hyping the scene. It worked, and the British press began calling attention to the label, which, in turn, made American A&R men take notice. Soon Soundgarden and Nirvana were signed to major labels and, when Nirvana's landmark album Nevermind was released, Pavitt and Poneman were not only rescued from bankruptcy, but were celebrities in their own right.

Pavitt used the publicity and capitol to strengthen his label and, always concerned with preserving local scenes, began signing bands outside of the Seattle area, such as D.C's Velocity Girl and the Afghan Whigs from Cincinnati. In the mid-'90s, with the alternative rock movement in full swing, the label Pavitt started as a newsletter some 15 years before was regarded as the essence of the uncompromising, D.I.Y. ethos of independent music. As of late, though, Pavitt has distanced himself from the label handing much of the day-to-day duties over to his partner Jonathan Poneman.