When filming, the special effects crew was unaware which tree would be uprooted. Therefore, every single miniature tree seen on set was built with miniature roots and individually planted one by one.
Instead of filming a real horse, Eiji Tsuburaya included a fake-looking puppet in the scene when Baragon tears through a farm. He was well aware of how it looked, but decided not to go with a more realistic effect because it was, by his own admission, "funny". Tsuburaya was well known for his jocular approach to his films, which frustrated some of the staff.
The film is often associated and said to be originated with the 1961 pitch by Willis H. O'Brien titled "King Kong vs. Frankenstein", also known as "King Kong vs. Prometheus". That would lead to the original "King Kong vs. Godzilla" (1962), but it is not the primary reason for this film being made. Henry G. Saperstein had previously distributed "Mothra vs. Godzilla" (1964) with UPA and announced that Toho and UPA would produce a Frankenstein vs. Godzilla film, thus the original idea for the film came from Saperstein's group. A Frankenstein vs. Godzilla story would be written before it was decided to create a new monster and make the Frankenstein Monster a more compassionate character.
The film was a Japanese-U.S. co-production. The versions released in Japan and the United States were nearly identical, though the U.S. version was about three minutes shorter. The international version for release outside the United States and Japan was longer and replaced the earthquake ending with Frankenstein battling a giant octopus.
As a huge fan of Frankenstein stories, this film is a personal favorite of director Guillermo del Toro. He has also recommended it on Twitter and cited the monster Baragon as one of his all-time favorite kaiju.