Notable for his longtime leadership of the Fantagraphics Books comics publishing house, Thompson also frequently contributed to Fantagraphics' magazines Amazing Heroes and The Comics Journal.
His interest in comic books began in his early years, during which he frequently wrote letters that appeared in the reader submission columns of Captain America, Iron Man, and other American comic books.
In 1996, his work on the comic books Palestine, Zero Zero, and The Acme Novelty Library earned him a Will Eisner Comic Industry Award nomination. In 2001, he was the recipient of an Inkpot Award.
He was born in Copenhagen, Denmark, and he lived in the Netherlands and West Germany before relocating to the United States in the late 1970s. When he died in his fifties of lung cancer, he left behind a wife named Lynn Emmert.
He and Mark Wilkinson are both prominent comic book artists.