Born in Japan, Shimomura is the son of Osamu Shimomura, winner of the 2008 Nobel Prize in Chemistry. He grew up in Princeton, New Jersey and attended Princeton High School.

At Caltech he studied under Nobel laureate Richard Feynman. After Caltech, he went on to work at Los Alamos National Laboratory, where he continued his hands-on education in the position of staff physicist with Brosl Hasslacher and others on subjects such as Lattice Gas Automata.

In 1989, he became a research scientist in computational physics at the University of California at San Diego, and senior fellow at the San Diego Supercomputer Center. Shimomura also became a noted computer security expert, working for the National Security Agency.

In 1992, he testified before Congress on issues regarding the privacy and security (or lack thereof) on cellular telephones.

He is best known for events in 1995, when he assisted with tracking down the "computer outlaw" Kevin Mitnick. Shimomura and journalist John Markoff wrote a book, Takedown, about the pursuit, and the book was later adapted into a movie of the same name.

Shimomura worked for Sun Microsystems during the late 1990s.

Shimomura presently lives in the Reno/Tahoe area.

Author Bruce Sterling described his first meeting with Shimomura in the documentary Freedom Downtime:

Kevin Mitnick's criminal activities, arrest, and trial were controversial, and have caused some computer industry journalists to raise legal and ethical questions concerning the events surrounding him. California author Jonathan Littman wrote a 1997 book about the case called The Fugitive Game: Online with Kevin Mitnick, in which he presented Mitnick's side of the story...a very different version from the events written in Shimomura and Markoff's Takedown. Amazon.com: The Fugitive Game: Online with Kevin Mitnick: Jonathan Littman: Books

In his book, Littman made allegations of journalistic impropriety against Markoff and of the legality of Shimomura's involvement in the matter, as well as suggesting that many parts of Takedown were made up for self-serving purposes by its authors.