Years before the online incarnation, Three-lobed Burning Eye was an independent literary magazine founded by Fuller and his friend Matthew Duncan while attending Bowling Green State University as creative writing students. Its original run lasted four printed issues from 1991-1993. The magazine is headquartered in Portland, Oregon and published by Legion Press.
In 1998, Fuller revived the magazine in name, with a direction more appropriate to the title, publishing decidedly more speculative fiction. Poetry, reviews, interviews, and even the editorial letter were considered distractions from a simple set of stories. At the time, the online format and an email submission system were not widely accepted practices for magazines.
Publishing frequency has changed over the last decade, from the original quarterly schedule, to triannual, to "2-3 times per year," with a few unintentional hiatuses, which have made the print anthologies less than annual. In 2010, the magazine released two issues in May and October. All issues remain archived online. Though the website design has changed using CSS development, the magazine retains its original intention of one story per page, without advertising. Print annual anthologies I-IV included four issues each of the online magazine, while volume V included five. These were available in limited black-and-white or color editions, available only during one pre-order period.
The magazine's name is a vague reference to H. P. Lovecraft's story "The Haunter of the Dark," in which the character Robert Blake concludes the story's narrative with his terrified record of what he can only glimpse of the approaching beast. "I see it-- coming here-- hell-wind-- titan-blur-- black wings-- Yog-Sothoth save me-- the three-lobed burning eye..." Despite the title's origin, the magazine has largely avoided publishing Cthulhu Mythos stories.