The band that would become Darkthrone formed during 1986 in Kolbotn, a small suburb of Oslo. They were a death metal group by the name of Black Death whose members were Gylve Nagell, Ivar Enger and Anders Risberget. In 1988 the band changed their name to Darkthrone and were joined by Ted Skjellum and Dag Nilsen. During 1988 and 1989 the band independently released four demo tapes: Land of Frost, A New Dimension, Thulcandra, and Cromlech.

They were subsequently signed to the independent record label Peaceville Records with a four album contract. In 1990 they recorded their first studio album, Soulside Journey. The album was cleanly-produced in a technical death metal style, although there were some elements of black metal present, in terms of the album's music and imagery.

Immediately following the release of this album, the band continued writing and recording new material. These demos were entirely instrumental but they demonstrated the band's gradual shift towards black metal. In 1997 they would be released on the compilation album Goatlord.

During 1991, Darkthrone adopted the aesthetic style that would come to represent the black metal scene, wearing corpsepaint and working under pseudonyms. Gylve Nagell became "Fenriz", Ted Skjellum became "Nocturno Culto" and Ivar Enger became "Zephyrous". In August 1991 they recorded their second album, which was released at the beginning of 1992 and titled A Blaze in the Northern Sky. The album contained Darkthrone's first black metal recordings, and Peaceville Records was originally skeptical about releasing it due to Darkthrone's extreme diversion from their original death metal style. After the album was recorded, bassist Dag Nilsen left the band, and is not credited anywhere on the album.

The band's third album, Under a Funeral Moon, was recorded and released during June–July 1993. It marked Darkthrone's total conversion to the black metal style, and is considered a landmark for the development of the genre as a whole. This album also marked the last album on which guitarist Zephyrous would perform.

It was followed by their fourth album, Transilvanian Hunger, which was released in February 1994. This was Darkthrone's first album to be recorded with just two members, Nocturno Culto and Fenriz. The band would remain a duo from this point onwards. Transilvanian Hunger was characterised by a very "raw" or "low fidelity" recording style and musical simplicity. The album's release caused some controversy: some of its lyrics were written by the infamous Norwegian black metal musician Varg Vikernes, and its booklet contained the phrase "Norsk Arisk Black Metal", which translates into English as "Norwegian Aryan Black Metal".

Darkthrone moved to another independent record label, Moonfog Productions, for subsequent releases. The label was run by Satyr of the black metal band Satyricon.

Their fifth album, Panzerfaust, was released in 1995. The album was received well, although its production, which is similar to that of Transilvanian Hunger, encountered some criticisms. Their sixth album, Total Death, was released during 1996 and is notable for featuring lyrics written by four other black metal musicians.

During the year 1995, drummer Fenriz was involved with numerous side projects. This included his solo ambient project Neptune Towers, recording an album with Satyr as the duo Storm, and playing bass on Dødheimsgard's debut album.

In 1999, Darkthrone released the album Ravishing Grimness, which featured "cleaner" production and a clear influence from the early work of Celtic Frost. This style would continue on their following album, Plaguewielder, which was released two years later in 2001. Its production style was "rawer", or as the band described it, more "necro".