During the 1960s and '70s, Stoll was assistant chief engineer at WBFO, a public radio station in Buffalo, New York.

Stoll has written three books as well as technology articles in the non-specialist press (e.g., in Scientific American on the Curta mechanical calculator).

Stoll played a decisive role in catching hacker Markus Hess in the 1980s, while Stoll was employed at the Lawrence Berkeley National Laboratory in California. He described those events in his book Tracking a Spy Through the Maze of Computer Espionage and the paper "Stalking the Wily Hacker", published in the professional journal Communications of the ACM. Stoll's book was later chronicled in an episode of WGBH's NOVA entitled "The KGB, the Computer, and Me" which aired on PBS stations in 1990.

In his 1995 book, Silicon Snake Oil, and an accompanying article in Newsweek Stoll called the prospect of e-commerce "baloney", and raised questions about the influence of the Internet on future society and whether it would be beneficial. Along the way, he made various predictions, e.g. about e-commerce (calling it unviable due to a lack of personal contact and secure online funds transfers) and the future of printed news publications ("no online database will replace your daily newspaper").

Stoll sells blown glass Klein bottles on the Web. , he is a "mostly" a stay-at-home dad. He teaches eighth graders about physics at Tehiyah Day School, in El Cerrito, California. Stoll was a regular contributor to MSNBC's The Site. Stoll is an FCC licensed amateur radio operator, callsign K7TA.