The band's name is derived from a section of lyrics in the Counting Crows song "Ghost Train"; "Took the cannonball down to the ocean/Across the desert from the sea to shining sea/I rode a ladder that climbed across the nation/Fifty million feet of earth between the buried and me".

The band was founded in 2000 in Raleigh, North Carolina by vocalist Tommy Rogers, guitarist Paul Waggoner, drummer Will Goodyear, guitarist Nick Fletcher (formerly of Empire Falls), and bassist Jason King. They selected their band name by taking a line of lyrics from the Counting Crows song, "Ghost Train".

Between the Buried and Me's first release was a three-song demo, containing the tracks "Use of a Weapon," "What We Have Become," and "More of Myself to Kill." These three tracks were re-recorded for the band's self-titled debut album, released through Lifeforce Records in 2002. The album includes the track "Arsonist," a protest against the beliefs and practices of the Westboro Baptist Church in Topeka, Kansas. The song "Aspirations" became the band's first music video. This album is not widely known and the songs from it are rarely played live. However, the release of it did gain the attention of Victory Records, to which they later signed. Victory Records reissued the album in 2004 as an enhanced CD.

In 2003, the band released their second studio album, The Silent Circus, featuring the singles "Mordecai", "Aesthetic", and "Camilla Rhodes". "Mordecai" was produced as their second music video. The album was re-released in 2006 with a live DVD of the band's performance at The Cat's Cradle in Chapel Hill, North Carolina on July 17, 2005. Mark Castillo played drums on The Silent Circus replacing Will Goodyear however, on the live DVD Blake Richardson, Dustie Waring, and Dan Briggs had already joined the band and recording for Alaska was already finished.

After the release of The Silent Circus, the band went through numerous members before the current lineup was assembled for the third album, Alaska. On drums, Mark Castillo was replaced by Jason Roe (later replaced by Blake Richardson). On guitar, Nick Fletcher was replaced by Shane Blay (later replaced by Dustie Waring). And on bass, Jason King was replaced by Kevin Falk (later replaced by Dan Briggs). Once the current lineup had been established, frontman Tommy Giles Rogers joked that it is the final lineup, and that he would quit if anymore lineup changes needed to take place. The band's lineup has not changed since that statement.

In the summer of 2005, Between the Buried and Me released their third studio album, Alaska. The title track "Alaska" became their third music video. The album released the songs "Selkies: The Endless Obsession", "The Primer", and "Backwards Marathon" as singles. Then in the following year, the band released The Anatomy Of, a collection of covers of bands that influenced Between the Buried and Me, including Metallica, King Crimson, Pantera, Queen, Pink Floyd, Earth Crisis, Counting Crows, and Soundgarden.

In September 2007, the band released their fourth studio album, Colors. The band has said that "it's a 65 minute opus of non stop pummeling beautiful music... we have described this release as 'new wave polka grunge.'" On their website, they have also described the album as "adult contemporary progressive death metal."

On November 6, 2008 the song "Prequel to the Sequel" was made available as downloadable content for Rock Band on Xbox Live marketplace and the PlayStation store.

On May 31, 2009, the group went into the studio to record their fifth original album The Great Misdirect. They have described one song as having "a noisy Coalesce breakdown, 3/4 Mastodon groove, 9/8 The Mars Volta, Queen chromatic build up, and Megadeth chorus". Tommy Giles Rogers had stated that they planned to "out do Colors".

In early 2006, Between the Buried and Me was on tour supporting Bleeding Through along with Every Time I Die and Haste the Day. They were also on the Ozzfest 2006 Second Stage. In late 2006, they were on the Radio Rebellion Tour headlined by Norma Jean.