In the original release, Batman and Spiderman appear as bosses. Batman was later replaced by a different enemy, while SEGA added a copyright disclaimer for Marvel Comics, who allowed Spiderman to stay in the game.

The Japanese version of the game was renamed "The Super Shinobi". Putting a US copy of the game into a Japanese console will still show the title as The Super Shinobi. Likewise, playing a Japanese copy of the game on a American or European machine will still show the title as Revenge of Shinobi.

Originally the developers of The Revenge of Shinobi intended Joe Musashi's master (the old man dying in the intro) to reveal himself to be the head of Neo Zeed and to be the game's true final boss. In addition to his martial arts skills, he would also have been able to summon earthquakes and falling rocks. The entire battle was sequenced and designed, but due to time constraints it never made it into the final game.

Naoko, Joe Musashi's bride, was named after the sister in law of designer and director Noriyoshi Ohba.

In an interview with game's director and designer Noriyoshi Ohba, he was told about how popular the game's composer Yuzo Koshiro’s music was. He commented:

"Yeah, it’s really a collection of some of his most famous songs. The Chinatown stage theme, in particular, is amazing. I remember getting goosebumps when [...] I listened to a demo tape of the Chinatown theme for the first time. I was impressed by his work, and we worked well together, so I asked him to do the music for Streets of Rage the following year."

Ohba's sound effects would also be re-used in later titles such as the Streets of Rage games.

According to a 2003 the Sega Meisaku series interview with the game's director/designer Noriyoshi Ohba, he was asked why the game wasn't a stealth game despite the name "Shinobi" implying the protagonist would be more stealthy. Ohba responded that this was probably due to the team wanting to show off "how cool and badass ninjas are" as they can jump higher than normal people and have stronger physiques.

According to a 2003 the Sega Meisaku series interview with the game's director/designer Noriyoshi Ohba, he was asked what kind of work directing the game specifically entailed. He responded that since he was the only planner/designer working on the game, he "basically had to be involved in everything" from the planning, to designing the gameplay system, to the art (including which backgrounds to use, among other things), etc.