The protagonist of Persona 3, canonically known as Makoto Yuki (having been used in other media and later confirmed as the default name in the 2023 re-release of Persona 3 Portable, along with choosing to select no name in Persona 3 Reload, defaulting to 'Makoto Yuki'), is a transfer student enrolling in Gekkoukan High School in Iwatodai City. He is an orphan whose parents died on the Moonlight Bridge in their car during a fatal incident a decade prior to the game.

In Persona 3, he is a silent protagonist, aside from technically speaking in battle in certain instances. While being a silent protagonist, he is very stoic, reserved and calm, gathered by the fact that he's faced death and his own mortality; he remains unmoved when walking under a green sky and being surrounded by blood pools and coffins everywhere at the beginning of Persona 3 or even when guns are pointed at him (such as by Aigis herself). He appears very introverted, distant and aloof since he only observes the conversations of his party members and only speaks when someone is directed at him for his opinion on the matter. At one point, Yukari Takeba raises her voice at him in frustration, calling him "Mr. Perfect" and saying nothing ever fazes him. She then apologizes for her behavior; he comforts her and she says that he "really is one-of-a-kind." His teacher, Isako Toriumi, comments that he is "kinda quiet, but real mature and intense looking" and that he uses proper grammar and punctuation online. Junpei Iori comments that all he does is wander around and talk to people, referencing what is commonly done during gameplay.

Many of his personality traits and reactions to certain situations are ultimately based on the player's actions and decisions. The primary choice has him being enthusiastic, upbeat and kind, engaging with as many Social Links as he can, each one rewarding him with stronger power in Persona fusion and combat. Likewise, the player can make him pessimistic, morbid and lonely, barely engaging with Social Links. In normal conversation, the protagonist's dialogue choices can range from attentive, to unobservant, to outright rude; generally only by being attentive would get a positive response from others. One of the protagonist's most common responses is "I don't care." Even when speaking to Pharos, the protagonist can respond saying that he doesn't care about his friends. These possible combinations of traits provide a wide range of various interpretations of his characterization. The same goes for any possible romantic interests the protagonist may partner with. The protagonist can choose from Yukari, Fuuka, Mitsuru, Aigis, Chihiro, Ms. Toriumi, Yuko and Elizabeth.

By the end of the game, as noted by Ryoji Mochizuki, the protagonist has found the answer to "life's greatest question," though the meaning of this statement is left ambiguous. As per the themes of Persona 3 and Aigis' own speech in the final scene, the answer is that simply having someone to protect is what gives one's life purpose. This is represented by the protagonist's resolve against Nyx, choosing to sacrifice himself by sealing it, all thanks to the many bonds he's forged with his friends.

In Persona 3 FES: The Answer, it's revealed the protagonist sacrificed his soul to become the Great Seal. Metis speculates the protagonist is content with his fate, and that he wished for the SEES to move on from him and live fulfilling lives. Nobody in the SEES objects with Metis' interpretation, and the Great Seal's statue does depict a smile despite his situation.