He played the navigator Pavel Chekov on the USS Enterprise in the original Star Trek television series and in the several movies that featured the original cast. He is of Russian Jewish descent, but his family changed their surname from Koenigsberg to Koenig, and claimed to be of Lithuanian descent during the McCarthy Era. He attended Grinnell College in Grinnell, Iowa.

After Chekov, his best-known role is the Psi Cop Alfred Bester on the television series Babylon 5. Koenig was the "Special Guest Star" in twelve episodes and, at the end of the third season, the production company applied for an Emmy nomination on his behalf. He was slated to play Bester on the spin-off series Crusade, but the series was cancelled before his episode was filmed.

In addition to acting, he has written a handful of episodes for TV shows: Star Trek: The Animated Series, Land of the Lost, Family and The Powers of Matthew Star. Walter Koenig has taught classes in acting and directing at UCLA, The Sherwood Oaks Experiment Film College, the Actor's Alley Repertory Company in Los Angeles and the California School of Professional Psychology.

He was cast as Chekov because of his resemblance to Davy Jones, to attract the younger audience, especially girls.

Koenig had heart bypass surgery in 1993. His role as Bester came out of that incident since his hospitalization forced him to bow out of a guest spot on Babylon 5. The series producer promised to make it up to him for the lost opportunity and got the Bester role later on.

In 2002, Koenig directed stage versions of two of the original Twilight Zone episodes for 4 Letter Entertainment.

Koenig is to reprise his role as Chekov in 2006 in an upcoming episode of Star Trek: New Voyages, an internet based Fan Series taking place in the 4th year of the original 5 year mission after TOS had been cancelled.