Shinobi II: The Silent Fury has received positive reviews, with common praise going towards the games improved level design, mechanics and difficulty compared to its predecessor.

The player begins the game as Joe Musashi (the Red Ninja), whose mission is to retrieve five elemental crystals that were stolen by the enemy and spread across different locations.

Depending on the stage, the player must use a specific ninja's ability in order to reach the location of the crystal.

Each of these skills can be used to destroy enemies, access secret areas, and obtain hidden health power-ups.

"[2] In 2011, Complex.com ranked it as the 18th greatest handheld game of all time, adding "it was definitely one of the reasons we were Sega fanboys/fangirls back in the day.