Following the demise of his old band Overcast in 1998, bassist Mike D'Antonio explored the underground Massachusetts hardcore punk and heavy metal scenes in search of members for a new band. In 1999, D'Antonio met Adam Dutkiewicz and Joel Stroetzel, guitarists for Aftershock. Dutkiewicz took the role of playing drums, while Stroetzel remained on guitar. The trio searched for a vocalist and eventually hired Jesse Leach, formerly of Corrin and Nothing Stays Gold. The now four-member band took the name of "Killswitch Engage," a name proposed by D'Antonio after watching an episode of the FOX program The X-Files entitled "Kill Switch". The episode's writer, William Gibson, came up with the title after a chance meeting with the industrial band Kill Switch...Klick; the two bands are otherwise unrelated.

While on tour with In Flames and Shadows Fall, Ferret Records took notice of Killswitch Engage's aggressive live show. The band signed with the record label and began recording their debut album.

The band's self-titled debut album was sufficient to earn them a deal with Roadrunner Records. Soon after signing with Roadrunner, the band decided to become a five-piece by bringing in former Overcast guitarist Pete Cortese. However, Cortese left soon after. In 2002 they released their second album, Alive or Just Breathing. This album greatly increased the band's exposure and placed them on the Billboard Magazine Top Heatseekers chart. The CMJ New Music Report described the record as "more addictive than crack cocaine that's been smothered in nicotine AND drenched with chocolate".[4] The band was once more made a five-piece when Dutkiewicz moved to guitars, with former Aftershock drummer Tom Gomes taking the vacant spot left. This move allowed the band's songs to include two guitars.

Leach left the band shortly after the release of Alive or Just Breathing. He had married his fiancée while on tour, but was separated from her due to the demanding tour schedule. Subsequently, Leach fell into a deep depression. During shows, he began screaming with more emotion than technique, and exhausted his voice. After the last show of their tour in Seattle, he sent the band an e-mail in which he explained his situation (see the World Ablaze DVD). This, coupled with the band's touring commitments, prompted Leach's departure in June 2002. Leach was replaced by Howard Jones, of Blood Has Been Shed, who has remained the band's vocalist since.

The new lineup played on the Road Rage tour in the UK and the Netherlands in 2002 with 36 Crazyfists, and continued touring throughout the rest of the year. In 2003, the band released the song When Darkness Falls, which appeared on the soundtrack of the 2003 horror film Freddy vs. Jason. The same year they also played the Ozzfest festival, after which drummer Tom Gomes left the band to live in Los Angeles with his wife and pursue their current band, (Something Of A Silhouette). He was replaced by Jones' fellow Blood Has Been Shed band member, Justin Foley, previously of jazz metal band Red Tide. Foley's first tour with the band was the MTV2 Headbangers Ball in 2003.

The band's third album, The End of Heartache, was released on May 11, 2004 and was the first release to feature Jones as vocalist. The album ultimately went on to sell more than 250,000 copies in the U.S. It also debuted in the top 40 of the Australian album charts on May 17, 2004, following a successful tour of Australia with Anthrax.

In late 2004, the band supported Slayer on their U.S. Jagermusic dates and headlined shows with From Autumn to Ashes, Eighteen Visions, and 36 Crazyfists. In addition, The End Of Heartache became the main single for the movie Resident Evil: Apocalypse. In December, 2004, the song was nominated in the Best Metal Performance category for the 47th annual Grammy Awards.

In late 2004, The End of Heartache was re-released as a special edition album, with a second disc featuring various live performances, a Japane