In 2029, the evil Emperor Garuda has taken over the United States of America, building a stronghold in the middle of the nation's "largest city".
To stop Garuda and avenge the innocent lives that were lost in his reign, ninja masters from the Iga clan, Lord Hayate is sent to infiltrate the dictator's well-guarded stronghold and kill him.
The player can run, crouch, climb ladders, attack, and jump like in most side-scrolling action games as well as hang onto an overhang and move under it. If the player has more than half of their vitality remaining.
The player's default weapon is a katana, which can be traded for a kusarigama and vice versa.
The kusarigama has a longer range than the katana and can be swung upwards diagonally and horizontally, but can only damage enemies from a specific distance and does not work as well at close range like the katana.
If the player picks up a weapon they already have, its attack power will be strengthened by an increment of one level (with up to three attack levels).
However, if the player takes too much damage, their weapon's strength will be reduced back to its previous level.
There is also the possibility to use both weapons, if the player starts with the kusarigama and collects secret power-ups hidden in some levels. The player can also obtain throwable shuriken and hand grenades as well, both which can only be used as long as the player's supply lasts before the player reverts to using the katana or kusarigama. All four weapons are obtained by destroying item boxes scattered throughout each stage, along with vitality potions.
Ninja Hero consists of five levels with 16 stages, with the first four levels being divided into three stages and the final level into two. The player fights numerous types of enemy characters throughout each level, including bosses and sub-bosses. Once a boss has been defeated it will explode, this explosion will heal players the closer they are to it, since actually the same amount of health from one level will be carried to the next one until either recovered with potions or by dying. The game ends if the player loses all of their vitality and only five chances are provided to continue.