Sebadoh began as an outlet for Lou Barlow's frustration with J Mascis, who refused to let Barlow contribute songs to any Dinosaur Jr. releases. In 1987, Barlow released Weed Forestin', a cassette of acoustic songs he had recorded at home on a four-track recorder, under the name Sentridoh. The cassette was sold at local Massachusetts record stores. Eric Gaffney contributed percussion to Weed Forestin', and when Barlow had a break from Dinosaur in 1988, the duo recorded The Freed Man, which consisted of songs by both songwriters. Also released as a homemade cassette, The Freed Man worked its way to Gerard Cosloy, the head of Homestead Records. Cosloy offered to release the cassette on his record label, and the tape was revised and expanded into a full-length album. Homestead released The Freed Man in 1989, and shortly after its appearance Mascis kicked Barlow out of Dinosaur, and Lou turned his attentions toward Sebadoh. A revised and expanded Weed Forestin' was released in early 1990; the two records were combined on the CD The Freed Weed later that year.

By the end of 1989, Sebadoh added a full-time drummer, Jason Loewenstein, on the suggestion of Gaffney. Sebadoh began playing concerts regularly, concentrating on Gaffney's material and throwing in a few Barlow songs for good measure. Where their albums were acoustic-oriented, their concerts were noisy ventures into post-hardcore and Sonic Youth territory. Over the course of 1990, the group was active only sporadically, deciding whether they wanted to pursue a full-fledged career; a few 7" singles of primarily acoustic material appeared that year. As of early 1991, the band began recording electric material, as evidenced by the EP Gimme Indie Rock! Released early in 1991, Sebadoh III was divided between Gaffney's electric songs and acoustic material by Barlow and Loewenstein. The band was prepared to embark on its first major tour when Gaffney abruptly left the band before its start. Barlow and Loewenstein carried on, initially performing shows as a duo, but soon hiring Bob Fay as a drummer. Upon the completion of the tour, Gaffney returned to the band, but during his absence, the direction of Sebadoh's music had shifted away from his songs and toward Barlow's.

Following a full-length national tour in the fall of 1991, Sebadoh recorded five of Barlow's songs as a demo tape that served as its gateway to contracts with Sub Pop in the U.S. and City Slang/20/20 in the U.K. Gaffney left the band at the end of the year, and the group again hired Fay as a replacement. With Fay, Sebadoh toured America and Europe in early 1992, recording the British EPs Rocking the Forest and Sebadoh vs. Helmet, which were combined later that year on the Sub Pop album Smash Your Head on the Punk Rock. Gaffney again returned to the band after Sebadoh released these recordings, with Fay again leaving the band. Barlow and Loewenstein had begun to tire of Gaffney's constant sabbaticals, and Lou returned to his Sentridoh project, releasing a series of EPs, 7" singles, and cassettes over the course of 1993 and 1994. Sebadoh released its fifth album, Bubble and Scrape, in the spring of 1993 and spent the remainder of the year touring behind the record, building their cult across America and Britain. Gaffney left for a final time in the fall of 1993 and Fay became his permanent replacement.

Before recording the sixth Sebadoh album, Barlow began a new band with John Davis called the Folk Implosion; the duo released three recordings over the course of 1994. Sebadoh returned with Bakesale, their first album without Eric Gaffney, in the summer of 1994. Boasting a somewhat more accessible sound, Bakesale became the group's most successful album to date, generating the near-modern rock hit "Rebound." The band took a break in 1995 and the Folk Implosion recorded the soundtrack to the controversial independent film Kids. Surprisingly, Kids spawned a genuine hit single with the haunting, hip-hop-tinged "Natural One," which climbed all the way into the Top 30 of the U.S. pop charts. In light of the success of "Natural One," Sebadoh's next record, Harmacy, was expected to be a hit upon its fall 1996 release. Though it didn't match commercial expectations raised by "Natural One," Harmacy expanded the success of Bakesale, becoming the first Sebadoh album to chart in the U.S..

Before the recording of their follow-up to Harmacy, Sebadoh replaced drummer Fay with Russ Pollard. After a string of delays, the revamped lineup released their first album, the cleverly titled The Sebadoh, in February 1999.