The story centers around a group of high school students looking for the truth behind all of Inaba's strange happenings. Over the course of the game, more classmates will join you and you'll meet a wide variety of people at school and part-time jobs.
Your group is lead by you and includes Yosuke Hanamura, Chie Satonaka and helped by an energetic creature that appears to be a living bear suit named Teddie in a world hidden behind television screens.
 Investigation Team
 Protagonist (known as Seta Souji in the manga adaptation)
- Persona: Has the ability to change personas freely, but Izanagi / Izanagi no Ookami are generally associated with him
- Arcana: Fool
- English VA: Johnny Yong Bosch
As in the tradition of other Shin Megami titles, the hero has no spoken lines or name, leaving the entire identity of the character up to the player. At the beginning of the game he moves to into Inaba to live with his uncle and cousin. Shortly after arriving he finds himself in a fog-shrouded world and instinctively summons his Persona, Izanagi. Like the protagonist of Persona 3, his alignment with the Fool arcana makes him the only member of the party who can actively change his persona in and out of battle.
In battle he uses two-handed swords and the occasional golf-club or baseball bat.
- Persona: Jiraiya and Susanoo
- Arcana: Magician
- English VA: Yuri Lowenthal (portrays the protagonist in Persona 3)
The son of the manager of the Junes outlet mall, Yosuke is ostracized by the families of local store owners but keeps a positive outward attitude despite this. In the investigation squad he plays a kind of second in command, tending to voice the player's choices as well as being a comedic relief, usually through (mostly self-inflicted to some extent) injury. The most vocal member of the team, he will piece together information for the player to interpret if they've yet to over the course of the investigation.
In battle be dual wields short swords, knives and spanners as well as garu and speed/evasion related spells.
- Persona: Tomoe and Suzuka Gongen
- Arcana: Chariot
- English VA: Tracey Rooney
An extremely athletic girl with a fascination in martial arts and a love of food, especially if its free, Chie is a classmate to Yosuke, Yukiko and the Protagonist. On the investigation team, she tends to overlook details and wants to rush into things which extends into all aspects of her. Often times she'll be on the delivering end of a kick to Yosuke, mostly played for laughs over a DVD he broke called "Trial of the Dragon."
Her love of martial arts extends into her combat styles and she'll kick enemies with various leggings and greaves. While not the most magic based character on your team, she provides bufu magic and strength-increasing spells.
- Persona: Konohana Sakuya and Amaterasu
- Arcana: Priestess
- English VA: Amanda Winn Lee
A wealthy and elegant girl whose family runs the historic inn of the town, she's outwardly shy towards most around her, bar Chie and is constantly asked by various boys from local schools if they could date her. She is also the top student of your class, unless you decide to hit the books early on.
In battle she takes the role of a spell caster, wielding fans that offer little physical power, with powerful agi and healing spells.
- Persona: Take-mikazuchi and Rokuten Maou
- Arcana: Emperor
- English VA: Troy Baker
A juvenile delinquent and local "legend," Kanji is most known for driving out biker gangs even though he's a high school fresh man. Under the tough exterior however he's socially inept and constantly second guessing himself and his own identity. His parents run a textile shop that he appears to help out in occasionally.
In battle he uses shields and other large objects, using his brute strength to slam enemies with them. His persona is capable of zio spells but is best noted for its amazing physical prowess.
- Persona: Himiko and Kanzeon
- Arcana: Lovers
- English VA: Laura Bailey
Rise is a former pop idol who decided to drop her career to work at her family's tofu shop, Marukyu. She is bubbly and flirts with the protagonist occasionally. In the TV World, Rise takes over Teddie's role as support, and as her S-Link levels up, she gains a wider variety of options to help the team.
- Persona: Sukuna Hikona and Yamato Takeru
- Arcana: Fortune
- English VA: Jessica Straus
Naoto is known as the "Detective Prince" when she first arrives at school and identifies herself as male to the group and the rest of the town, even though she is actually female. Naoto joins the police force's investigation of the murders in Inaba, but her ideas are pushed aside and she is often treated as a child. She initially sees the protagonist's investigation as a joke and laughs at it, but after the police begin to treat her unfairly, she begins to take it more seriously. Unlike the other victims of the Midnight Channel, Naoto willingly put herself at risk of be kidnapped by appearing on television for an interview about the case, hoping that she would be successful in finding the real killer.
Naoto's persona has access to powerful almighty spells as well as light, dark, and some physical attacks, and as a result uses large amounts of SP. In battle, Naoto uses revolvers.
- Persona: Kintoki-Douji and Kamui
- Arcana: Star
- English VA: Dave Wittenburg
Teddie is the aptly named stuffed bear character that you first encounter in the TV World. He initially acts as support for the team by giving them special glasses to help them see through the fog and aiding them in battle. Once Rise joins the team, she will take over Teddie's role as support and Teddie will be able to fight alongside the protagonist and other characters. Teddie's S-Link focuses on his search for his origins and who (or what) he really is. The protagonist helps Teddie realize his role throughout the progression of the game, meaning that Teddie's S-Link will progress and level up on its own, making his evolved persona easy to obtain.
In battle Teddie uses his claws (or gloves) to strike enemies and wields powerful bufu magic, as well as some effective healing spells.
 Yasogami Students and Staff
- Arcana: N/A
Third year. Works at Junes after school. A friend of Yosuke's and daughter of the local liquor store owners, she is bothered by her parents for working for "the enemy" but appears to harbor no ill-will towards Yosuke or her family over this.
- Arcana: Hanged Man
First year. Found outside Classroom 1-1. Saki's younger brother and a bit of an outcast at school, mostly keeps to himself. He is the Hanged Man Arcana Social Link.
- Arcana: N/A
Second year. Seen on the second floor of the Classroom Building. Overweight girl who is usually seen hunched over a large pile of food in her appearances outside of school
- Arcana: Strength
Second year. Hangs out with Kou outside Classroom 2-1. One of the hardest working and best soccer players at the school, he's often seen on or around the fields when he's not hanging out with Kou. He is one of the two options the player has for the Strength Arcana social link.
- Arcana: Strength
Second year. Hangs out with Daisuke outside Classroom 2-1. Yasogami's star basketball player, he can be found practicing with the team after school whenever possible. Along with Daisuke, he is the Strength Arcana social link.
- Arcana: Moon
Second year. Lounges at the shoe locker area. First introduced through the Strength social link, Ai is a near-failing student who often skips class to go shopping, she's often scolded by teachers. She is the Moon Arcana social link and requires level 3 courage to approach her.
- Arcana: Sun
First year. Found near the stairs of the Classroom Building's second floor. A member of the school's band, she plays trombone but is often given the club's paperwork due to a lack of musical ability. Quick to apologize, she tends to be pushed around by the club as a result, ending in her practicing alone after the club meetings have adjourned. She, and Yumi Ozawa, are the Sun Arcana social link, though unlike Kou and Daisuke of the Strength link, only one is ever seen as opposed to meeting with both.
- Arcana: Sun
Second year. Found near the stairs of the Classroom Building's second floor. The best actor in the school's drama club, she prides her self on her ability to become another person for her roles. Somewhat overbearing to the other members, she often overrides the club presidents decisions in order to see what she thinks will turn out as a better performance. With Ayane, she is an option for the Sun Arcana social link.
- Nicknamed King Moron by many students.
Philosophy Teacher, 2-2's Homeroom adviser. An offensive and strict teacher, Kinshiro will commonly insult his class while commenting on the state of modern society, namely the culture of teenagers. He also proclaims that the students work is ultimately futile as they'll never succeed in life unless they leave the town to use what they learned in the outside world, which many won't.
 Kimiko Sofue
Also known as Queen Tut, she is Yasogami's World History Teacher. Can be found on the Classroom Building's 2nd Floor stairwell. Like her predecessor in Persona 3, she is absolutely fascinated by history and even dresses like Egyptian royalty. Eccentric in her studies, she will sometimes ask the protagonist to find items that can be gained in the TV world. Will sometimes make comments about a fellow teacher at another school who dresses as a samurai.
 Mr. Kondo
P.E. and English Teacher. Also the adviser for the Basketball and Soccer Club. Occasionally quizzes students in the P.E. class with extra laps being the punishment for a wrong answer.
 Mr. Yamada
 Mrs. Nakayama
Math Teacher. Usually found on the Classroom Building, 3rd Floor.
 Mr. Hosoi
Classical Literature Teacher.
Biology Teacher, Morooka's replacement as 2-2's Homeroom Adviser though the complete opposite of her predecessor. Laid back and will often trail off in her lectures and talk about upcoming vacations or rather inappropriate topics for school. Due to this nature many of the students dislike her, some calling her worse than Morooka. She dislikes Rise and other teen idols, calling them "inexperienced jailbait" which may be part of the class' distaste for her, as Rise is a popular idol.
 Other Characters
- Arcana: Justice
The cousin of the Main Character and Ryotaro's only child, she is very young and innocent but due to her father's work and mother's death is often left to fend for herself at home. While at home she either makes simple meals, cleans or watches TV. Over the course of the game she will see the protagonist as an older sibling and often calls him "Big Bro," when welcoming him home in the afternoon.
Over the course of her social link, the protagonist helps Nanako realize that her father is just as upset about the loss of her mother as well as come to terms with how busy he is due to his work. It is also revealed that she has some form of stomach virus through her and Ryotaro's social links.