The film was produced as a commemorative work for Toho's 35th anniversary, made in partnership with Rankin/Bass Productions, since Toho's license to use King Kong (obtained for King Kong vs. Godzilla) was only valid for five years and set to expire soon.

An earlier project titled 'Operation Robinson Crusoe: King Kong vs. Ebirah' was planned the previous year but negotiations fell through, leading to a new version incorporating Dr. Who and Mechani-Kong to align with the concurrent Rankin/Bass animated TV series, The King Kong Show.

Arthur Rankin Jr., head of Videocraft International which produced the King Kong animated TV series, served as technical advisor on the film.

Linda Miller, who played Susan Watson, had no acting experience and was working as a model when producer Arthur Rankin Jr. spotted her in a gravure photoshoot in the magazine Josei Seven and cast her.

Mie Hama was cast as Madame Piranha as a last-minute replacement after original choice Akiko Wakabayashi did not renew her Toho contract and went freelance.

Because Linda Miller was not a member of the Screen Actors Guild, her voice was redubbed by Julie Bennett for the English version, while Rhodes Reason (who was a SAG member) was able to re-dub his own character; Miller was reportedly upset she wasn't invited to redub her own lines.

The character of Gorosaurus was designed as a deliberate homage to the Tyrannosaurus fight from the original 1933 King Kong, even sharing its three-toed forefeet, leading the filmmakers to classify Gorosaurus in-universe as a species of Allosaurus.

Because the film's monsters were designed at a smaller scale (20 meters) than Godzilla (50 meters), the miniatures were built at a larger 1/15 scale instead of the usual 1/25 scale used in Godzilla films, resulting in more detailed models.

The Tokyo Tower miniature set was specially engineered with welded steel framing instead of the usual wood-and-nails construction, since the design required two suited monsters to climb and fight on it without collapsing.

The film used a unique five-strip compositing process combining standard footage, a mask film, and three RGB monotone films to eliminate the flickering edges typical of bluescreen compositing; effects artist Koichi Kawakita considered the results excellent but the process was never used again due to its inefficiency.

This was the first Toho film to use a radio-controlled, self-propelled Type 61 tank miniature with an internal engine capable of turning, whereas earlier tank miniatures could only move in straight lines pulled by piano wire.

Mechani-Kong's roar sound effect was later reused for the capsule monster Windam in the Ultra Series show Ultraseven.

The stock footage of Gorosaurus living on Monster Island in the 1969 film All Monsters Attack was reused footage taken directly from King Kong Escapes.

Producer Tanaka Tomoyuki's idea for Mechagodzilla in Godzilla vs. Mechagodzilla reportedly originated from him recalling Mechani-Kong and wondering if a similar robot could be built for Godzilla.

Toho originally considered including King Kong in an early draft of Destroy All Monsters (1968) but dropped him because the studio's rights to the character were expiring.

In the early 1990s, Toho considered a project called Godzilla vs. Mechani-Kong, reviving Mechani-Kong as Godzilla's opponent after a planned Godzilla vs. King Kong remake fell through, but the project was cancelled when it became clear that even using King Kong's likeness would require difficult rights negotiations.

Despite being praised for its high level of special effects craftsmanship, the film was not a box office success in Japan, and younger audiences reportedly preferred its co-feature, the Ultraman feature film, at the time.