Batman Begins is an action-adventure game incorporating both beat 'em up and stealth elements. The player controls Batman from a third-person perspective, who has access to several gadgets that can be put to good use during both combat and stealth segments. These include batarangs, smoke grenades, flash bang grenades, and an 'HF Transponder', which summons bats to gather around and incapacitate enemies with "fear" (a gameplay mechanic unique to this game). During stealth segments, the player can interact with the environment to create various circumstances that scare off enemies, such as explosions or dropping crates near them, making them easier to subdue. Fear also plays a role in the combat segments, where, if the fear bar is filled, it allows the player to finish off the last remaining enemy with a single hit. The overall stealth gameplay is reminiscent of the Splinter Cell series.
Aside from the combat and stealth segments, the game also incorporates several combat racing sections where the player drives the Tumbler. The game features several alternate costumes for Batman to wear, which are unlocked after completing the main story. Aside from the story, there is a "Gallery of Fear", where the player can view various enemies and villains they have encountered throughout the game and read their bios.