Shinji Ikari is the protagonist of Neon Genesis Evangelion and a 14-year-old boy whose father is Gendo Ikari, the Commander of the special agency NERV. Having lost his mother, Yui, at a young age and lived apart from his father for a long time, he lacks self-confidence and possesses a delicate personality that fears human interaction. Suddenly summoned by his father, he is ordered to become the pilot of Evangelion Unit-01 to fight the "Angels" attacking humanity. Although he initially refuses to fight, he grows little by little through interactions with his comrades and those around him. However, with every battle, he suffers psychological distress and struggles deeply with his distance from others and his own reason for existing. His emotional fluctuations and growth are the central axis of the story; his struggle to move forward despite his weaknesses, symbolized by his iconic phrase "I mustn't run away," resonated with many viewers. Shinji is depicted not as a simple hero, but as a person with human-like weaknesses and kindness.

Asuka Langley Soryu (known as Asuka Langley Shikinami in the Rebuild of Evangelion films) is the exclusive pilot of Evangelion Unit-02. A 14-year-old raised in Germany, she is one-quarter Japanese and three-quarters German. A child prodigy with superior intelligence, she graduated from university at a young age. She has a bright, aggressive, confident, and competitive personality, taking great pride in her own abilities. On the other hand, she harbors deep loneliness and emotional scars from losing her mother in childhood, giving her a delicate side that makes her extremely loath to show weakness to others. She and the protagonist, Shinji Ikari, develop a complex relationship, frequently clashing while building a significant bond throughout the story. As a pilot, she boasts exceptional piloting skills, but her mental state heavily influences her synchronization rate with the Eva, leading to struggles in the latter half of the story. Her appeal lies in her human-like portrayal of both strength and fragility, making her one of the most popular characters representing Evangelion alongside Rei Ayanami.

Rei Ayanami is the exclusive pilot of Evangelion Unit-00 and one of the central figures of the story. A 14-year-old girl, she is taciturn and expressionless, having almost no interaction with others and rarely showing emotion. However, she hides kindness and a caring heart within, gradually showing human-like emotions through her interactions with the protagonist, Shinji Ikari. While she places great trust in NERV Commander Gendo Ikari, a significant truth regarding her birth is hidden, deeply connected to the Human Instrumentality Project and the secrets of the Evas. Rei is a being created based on the genetic information of Yui Ikari and the soul of the second Angel, Lilith; she is a unique existence with multiple identical clones prepared. Her quiet, mysterious atmosphere and the major decision she makes at the end of the story had a profound impact on the entire work. With a personality that contrasts sharply with Asuka's, she continues to receive high support as a representative popular character of Evangelion.