Successfully complete one of the following tasks to get a trophy:
- For Naoko. For peace. Shinobi forever! (Gold): Rescue Naoko without using a continue.
- A Clash With Evil (Silver): Defeat the Round 1 boss without using the 8-way Shuriken Attack.
- Brawn Over Ninjutsu (Silver): Finish 6-1 without using any Ninjutsu.
- Beautiful Assassin (Bronze): The dancing lady in Chinatown must not be defeated!
- Shinobi Has Fallen (Bronze): How was that dive into the waterfall?
- Shuriken Rain (Bronze): Use 300 Shuriken.
- Behold! Emblem of Blue! (Bronze): Appreciate the SEGA logo.
- The Traps of Neo Zeed (Bronze): Trigger 10 bombs.
- Miraculous Ninja Arts (Bronze): Use all four types of Ninjutsu in one game.
- Impenetrable Wall (Bronze): Guard 10 attacks with your cross-guard.
- Shuriken Starburst (Bronze): Demonstrate Joe Musashi's 8-way Shuriken Attack.
- Shinobi Watches (Bronze): Stand atop the brick pillar in 3-1. Ninja style!