Founded after the 1984 Stop the City protests, the magazine was launched in the summer of that year by an editorial collective consisting of Alan Albon, Richard Hunt and Marcus Christo.
However the diversity that many saw as the publication's greatest strength quickly led to irreconcilable arguments between the essentially pacifist approach of Albon and Christo, and the advocacy of violent confrontation with the State favoured by Hunt.
During the 1990s Green Anarchist came under the helm of an editorial collective that included Paul Rogers, Steve Booth and others, during which period the publication became increasingly aligned with primitivism, an anti-civilization philosophy advocated by writers such as John Zerzan, Bob Black and Fredy Perlman.
During this period the magazine expressed sympathy for the criminal activities of Ted Kaczynski and published a notorious article entitled "The Irrationalists" that supported actions like the Oklahoma City bombing and the sarin gas attacks carried out by the Tokyo based Aum cult.
Starting in 1995, Hampshire Police began a series of at least 56 raids, code named 'Operation Washington', that eventually resulted in the August to November 1997 Portsmouth trial of Green Anarchist editors Booth, Saxon Wood, Noel Molland and Paul Rogers, as well as Animal Liberation Front (ALF) Press Officer Robin Webb and Animal Liberation Front Supporters Group (ALFSG) newsletter editor Simon Russell.