In Tenchu: Dark Secret, you play as Rikimaru or Ayame, two ninja who must protect a princess in feudal Japan. They do this through a variety of missions where they must sneak through areas unseen by guards and assassinate targets, which frequently takes the form of boss fights along with other types of missions, such as defense. Unlike the other games in the series, this is played from a top-down perspective.

The top screen serves as the main gameplay area where you see your character, environment, enemies, etc. It also has your chi meter which tells you how close the nearest enemy is and whether they detect you. The lower screen is used for the map, selecting items, and for stealth kill animations which are played when you strike an enemy that hasn't seen you.

Items including series staples like mines, throwing stars and rice balls and include a new trap combo bonus for doing things like using a mine to blow an enemy into another trap.