In 1997, guitarists Torsten Wolf and Volker Trost joined with bassist Pablo J. Tammen to form a band called Timezone. Shortly after recording a demo, however, the band split up. Soon thereafter, the lineup was rounded out with singer Jioti Parcharidis, drummer Apostolos "Laki" Zaios, and keyboardist Dirk Marquardt, and called themselves Human Fortress.
After recording a demo in 1999, the band got to work on their debut album, which was completed in the summer of 2000. They entered a talent contest sponsored by a popular German metal magazine. Their song "The Dragons Lair" was released on a compilation CD for the contest, and was subsequently voted "Favorite Track" by online fans. Due to this recognition the band reached a deal with Limb Records, and released their debut album Lord of Earth and Heavens Heir.
2003 saw the release of the band's second album Defenders of the Crown, this time on Massacre Records. The recording process included guest performances by members of the bands Galloglass, King Leoric, and Meridian Zero. After this album, guitarist Volker Trost left the band and was replaced by Frank Sawade.
In 2007, the face of Human Fortress changed once again, as singer Jioti Parcharidis and drummer Apostolos "Laki" Zaios left the band. They were replaced by Carsten Frank and Arndt Krone, respectively. Human Fortress released their third CD, Eternal Empire, on April 25, 2008. Arndt Krone and Torsten Wolf left the band in the same year, the first being replaced by drummer Vincent Gongala.
In 2009 the band announced that Frank Sawade, Pablo J. Tammen, Dirk Marquardt and Vincent Gongala would form a new band called Ember Sea with singer Eva Skamira, continuing the new style adopted for the third album, and that the former band members Jioti Parcharidis, Torsten Wolf, Volker Trost and Apostolos "Laki" Zaios, reinforced by newcomers Ingmar von Berg and Dirk Liehm, would continue as Human Fortress in the style of the first two albums. However, singer Jioti Parcharidis left again due to health problems in the beginning of 2010. In July 2013, following a 5 year hiatus, Gus Monsanto became the Human Fortress' new singer, and the band signed with AFM Records. The band's fourth CD, Raided Land, was released in November of that year.
The band began recording their fifth album in July 2015, "Thieves of the Night", released in March 2016,