Starting in this film, All Effects Company took over and worked on the animatronic effects for the turtles and Splinter costumes. Jim Henson's Creature Shop was the company who worked on the mutant creatures in the previous two movies.

This film was originally going to be followed by a fourth installment in the franchise, "TMNT: The Next Mutation." In this concept, the Ooze that transformed the Turtles and Splinter was still in their bodies, causing a much more drastic second mutation. Another plan that was discussed was to add a fifth turtle named Kirby (named after comic artist Jack Kirby). However, the project got stuck in development and plans for a fourth theatrical live action movie fell apart. The concept of having the Turtles mutate into creatures did see the light of day in the 'New Mutation' saga of the Teenage Mutant Ninja Turtles (1987) cartoon. Later, the live action "Next Mutation" installment moved to television in a live-action series produced by Saban, titled Ninja Turtles: The Next Mutation (1997). This series delivered on the promise of a fifth turtle, but changed it to a female turtle named Venus Di Milo.

Mark Caso (The performer inside the Leonardo costume), is the only cast to return from Teenage Mutant Ninja Turtles II: The Secret of the Ooze (1991). Brian Tochi (The voice of Leonardo) and Robbie Rist (The voice of Michaelangelo) are the only actors who appeared in all three movies in the trilogy. Corey Feldman who appeared in Teenage Mutant Ninja Turtles (1990) makes his return as the voice of Donatello.

Producers invited Corey Feldman to reprise his role from the first film as Donatello. The filmmakers told Corey they felt bad about not casting him for Teenage Mutant Ninja Turtles II: The Secret of the Ooze (1991). However, when Corey asked for more money than the $1500 he was paid on Teenage Mutant Ninja Turtles (1990), Corey was told, "yeah, but you were in rehab." Corey was denied the raise, and was again paid only $1500.

The concept for this movie is loosely based on a story called "Masks" from issues #46 and #47 of the original Mirage comics. The story features the Turtles and Renet traveling back to Feudal Japan to fight an evil shogun and engage in samurai battles.

At one point in the movie, one of the turtles refer to Walker (Stuart Wilson) as the "Zorro dude". Wilson later starred in The Mask of Zorro (1998) as Zorro's arch-nemesis, Don Rafael Montero.

In the original comics, the Time Scepter is normally associated with Renet, the timestress apprentice of Lord Simultaneous. She often encounters Savanti Romero. None of these characters appear in this film.

At the time this movie was released, Golden Harvest thought the franchise had reached the end of its movie career. The project went forward with low expectations, little fanfare, and a modest $17 million budget.

This film brings back the character of Casey Jones, who wasn't in the second movie.

This is film is part of a multi-media Feudal Japan Ninja Turtles event with the "Masks" story first appearing in the Mirage comics in 1992, the third film released in early 1993, and the Turtles and Splinter traveling back to Feudal Japan to fight Shredder in a late 1993 episode of the Teenage Mutant Ninja Turtles (1987) cartoon. Since then, traveling back to Feudal Japan has been a staple for the Turtles.

In the Teenage Mutant Ninja Turtles franchise, Mitsu was supposed to appear as one of the fighters in the Super Nintendo game, Teenage Mutant Ninja Turtles: Tournament Fighters (1993). However, the character in the game was renamed Aska.

The animatronic heads of Michaelangelo and Leonardo from this movie are now in the hands of an obsessed Turtles fan named Michele Ivey. She bought them for $3800 US.

This is the only live action turtles movie where a theme song was not specially written for it.

Matt Hill, who was the suit actor for Raphael in this movie, is the only actor who to reprise his role for the next installment, Ninja Turtles: The Next Mutation (1997). However, in Next Mutation, he was not the suit actor, but provided the voice for Raphael.

In the Teenage Mutant Ninja Turtles franchise, "Turtles in Time" is the theme for the first Super Nintendo game, the second arcade game, the third movie, and the fourth video game made for a Nintendo home console (the first three were made for the original NES).