Born Gerald Alexander Abrahams, his family changed their name to Anderson in 1939. Anderson worked as an editor at Gainsborough Pictures until he was conscripted in 1947, and performed his national service in the Royal Air Force where he was trained in radar operation. He returned to Gainsborough until the studio went out of business in 1950.

In 1957 he formed AP Films (for Anderson-Provis) with commercial maker Arthur Provis. The studio was based in Slough and struggled at getting work until a puppeteer named Roberta Leigh brought a puppet made of toilet paper rolls to them. They made a series about the character and its ability to lengthen its limbs, titled The Adventures of Twizzle. Provis and Leigh also worked with Anderson on Torchy the Battery Boy before splitting to make Adventures of Sara and Hoppity (1961) and Space Patrol (1963).

Anderson made sales of his early puppet shows to Associated-Rediffusion (the London weekday ITV station) but soon found Lew Grade and his Associated Television company (London weekends and Midlands weekdays) to be a better market, with Grade acting as a patron. He surrounded himself with highly skilled technicians who shared his ex-RAF background, and increasingly detailed models of aeroplanes and spaceships would feature in his productions.

After Twizzle and Torchy Anderson directed and produced the rarely seen feature Crossroads to Crime (1960), the failure of which frustrated his wish to move into live action. His next series was a Western called Four Feather Falls from an idea by Barry Gray, who would go on to compose for all of Anderson’s work until the mid-seventies. At the same time his studio perfected Supermarionation; a system of controlling the puppets through synching the mouth to pre-recorded lines via a solenoid valve within its head. His next series, Supercar (1961) was "filmed in Supermarionation" and struck a format Anderson would return to again and again; an advanced vehicle benevolently rescuing innocents.

Fireball XL5 (1962), Stingray (1964), Thunderbirds (1965), Captain Scarlet (1967), Joe 90 (1968) and The Secret Service (1969) all featured organisations protecting the world. Lew Grade cancelled his order for The Secret Service after viewing the pilot, and Anderson moved into live action production with the feature Doppelganger (1969) and series UFO (1970). His next show was the most conventional yet, a detective series called The Protectors (1972).

Trying to capitalise on the success of UFO, Anderson had the idea of the alien invaders casting the moon off into deep space, carrying moon base and its crew along the way. This became the genesis of Space: 1999 (1975). Unfortunately for Anderson, while he had the support of Lew Grade, a sale to one of the American television networks had eluded him, with his series having to be laboriously marketed  to individual stations. A scathing review of the physics of the series by Isaac Asimov in TV guide made this more difficult. During the first series of Space: 1999 his marriage to Sylvia Anderson (nee Thamm) broke up, with the loss of her collaboration a producer named Fred Freiberger was brought in to guarantee sales for a second year. Freiberger had performed a similar function on the third series of Star Trek, and his changes were not greeted by fans. A third year was planned but not produced.

Anderson returned to puppetry with Terrahawks (1983) and then tried stop motion with Dick Spanner, P.I. (1987). Space Precinct (1994) was a live action series set in a police department in Altair, Lavender Castle (1999) combined stop motion and computer generated imagery, and the poorly regarded anime Firestorm (2003) used CGI for vehicles and cell animation for characters. His final series was a return to Captain Scarlet (2005), now created with motion capture and CGI animation.

Gerry Anderson disliked working with puppets and found their technical limitations frustrating. However he remained innovative throughout his puppetry phase in the 1950s and '60s, many techniques developed by APF/Century 21 Productions would become standard throughout the industry. While working in film, Anderson's company devised a method of  recording on videotape via the same lens exposing the filmed images, allowing instantaneous playback. Adding some exciting clips from the show during the opening credits was another innovation and became known as "Andersonizing" the material.

Gerry Anderson announced he was suffering from dementia in June 2012 and was a celebrity ambassador for the Alzheimer’s Society.  His condition was described as “rapidly deteriorating” and he was moved to a home in October. His family announced his death on 26 December 2012, but no cause was given. He survived by his wives Mary and Sylvia, and his four children.