The game was ported to the Nintendo Entertainment System in 1990. This conversion was titled Teenage Mutant Ninja Turtles II: The Arcade Game in order to avoid confusion with the previous NES game based on the franchise. The Japanese Famicom version was titled Teenage Mutant Ninja Turtles, without a number nor a subtitle, due to the fact that first NES game was localized in Japan under a different title.

The Snowfield level added to the NES port, with the boss character shown here.

This version includes two new levels (the first part of Scene 3 and all of Scene 6), which feature new enemy characters, including two new bosses: Tora (a dog-like "blizzard beast") and Shogun (a robotic samurai), both characters created for the game. Most of the original stages from the arcade version were extended as well and the second half of Scene 3, the parking garage stage, replaces the arcade version's end battle with Bebop and Rocksteady with a battle against the mutated fly form of Baxter Stockman. The NES version of the game was once slated for release on the Wii Virtual Console, but was canceled. The NES port appeared in Nintendo's PlayChoice-10 arcade system.

The NES version featured notable product placement advertising: Pizza Hut logos. The rear cover of the instruction manual provided a coupon for the restaurant, with an expiration date of December 31, 1991.