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Shinji Matou is the biological son of Byakuya Matou, belonging to the declining Matou mage family. Originally known as Makiri, the Matou lineage suffered deteriorating magical capabilities over generations, leaving Shinji born without functional Magic Circuits. This rendered him incapable of practicing magecraft despite his heritage. Byakuya married a woman with an inheritor sorcery trait hoping to restore the family's magical potential; Shinji's birth without circuits marked a further disgrace.

Shinji initially believed himself destined to become the Matou heir. This perception shifted when Sakura Tohsaka was adopted into the family as a potential heir. Shinji rejected Sakura as an outsider at first, though he gradually accepted her while masking his feelings behind teasing due to his arrogant nature. Discovering the Matou "worm pit," where Zouken Matou subjected Sakura to Crest Worms for magecraft training, shattered his worldview. Following this, Byakuya distanced himself, and Shinji redirected his anger toward Sakura, blaming her for usurping his perceived birthright. After Byakuya's death, Shinji's mistreatment escalated to physical and sexual abuse, which Sakura endured out of pity and guilt.

Academically successful, Shinji served as vice-captain of the archery club at Homurahara Academy, maintaining popularity despite his chauvinistic and narcissistic tendencies. He formed an estranged friendship with Shirou Emiya during middle school, often deriding Shirou's selflessness while covertly protecting him from exploitation. Shinji disapproved of Sakura's growing closeness to Shirou, fearing it would diminish his control over her.

When the Fifth Holy Grail War began, Shinji sought to prove his worth to Zouken. Sakura had summoned the Servant Rider but refused to fight. Shinji persuaded Zouken to grant him temporary command of Rider using a fabricated Command Spell book, the Book of False Attendant. Lacking innate magical energy, Shinji relied on Rider's Blood Fort Andromeda boundary field to drain life force from students at Homurahara Academy to sustain her.

In the Heaven's Feel route, Shinji's actions intensify. After Rider's initial defeat, he kidnaps Sakura, forcing her to create another Command Spell book. He holds her hostage at the school, demanding Shirou fight Rider. When Rin Tohsaka and Archer intervene, defeating Rider again, Sakura revokes Shinji's control. Enraged, Shinji uses alchemical knowledge to trigger Sakura's Crest Worms, causing her to lose control and activate Rider's boundary field uncontrollably. Later, confronting Sakura at the Matou residence, Shinji taunts her about his history of abuse, provoking her into killing him.

In other routes, Shinji's outcomes differ. In the Fate route, Illyasviel von Einzbern and Berserker kill him after Rider's defeat. In Unlimited Blade Works, he allies with Kirei Kotomine and receives Gilgamesh as a Servant after Rider's death. Gilgamesh manipulates him into becoming a vessel for the Holy Grail by implanting Illyasviel's heart, resulting in his transformation into an amorphous mass before Rin rescues him.

Outside the main timeline, Shinji appears in Fate/EXTRA as a distinct character sharing the name and appearance. This eight-year-old gaming champion participates in the Moon Holy Grail War under the mistaken belief it is a virtual game. He maintains a sibling-like dynamic with his Servant, Rider, remaining unaware of the war's lethal stakes until his defeat.

Shinji's personality combines arrogance, impulsiveness, and an inferiority complex stemming from his magical incapacity. He exhibits chauvinistic attitudes and a sense of entitlement, particularly toward Sakura, whom he views as family property. Despite his flaws, he demonstrates intelligence, dedication to pursuits like archery and alchemy, and a persistent desire for validation. His relationship with Shirou is marked by ambivalence; he values their friendship but resents Shirou's moral integrity and growing bond with Sakura.