The arcade version can be played by up to two players. The game's controls consist of an eight-way joystick and two action buttons. Similarly to Kung-Fu Master and Rush'n Attack, the player jumps by holding the joystick upwards instead of having a dedicated jump button like other side-scrolling action games. Instead, one button is used to swing the sword at enemies and the other to hold the shield to block enemy attacks, including projectiles such as throwing-knives and arrows. The shield can be held towards the player while standing or crouching, as well as upwards vertically and diagonally. Some enemies will throw magic balls which cause the player to lose their sword and shield if they block. During these instances, the player will fight barehanded, with the sword and shield buttons used to punch and kick respectively. The sword and shield will appear on-screen after some time, allowing the player to recover them. Power-ups include floating hearts that restore the player's health and jumping spots where the player can jump higher than usual.
The game consists of six stages, where the player will face the usual series of weak enemies, as well as a sub-boss at the middle of each stage and a boss at the end. The player is allowed to start the game at any of the six stages. However, the player must play through the entire game again after defeating the final boss, Achilles, in order to see the true ending (similarly to Ghosts 'n Goblins). The player can continue after a game over depending on the dip switch settings.
The NES version of Trojan features several significant changes to the game, such as the addition of new power-ups and hidden rooms, an additional boss battle on the final stage against a pair of characters known collectively as King Shriek, and an alternative versus mode, where two players compete against each other in a first-to-three-rounds match, making it Capcom's first attempt at the fighting game genre. Player 1 controls the main character, while Player 2 controls the enemy character, whose abilities are identical to the main character. While the version in Capcom Classics Collection Vol. 1 is a direct emulation of the original arcade game, it also allows the option to assign one of the action buttons for jumping in addition to using the directional pad or the analog stick.