Each short story of which the series consists describes the suffering of a different individual caused by one or more antagonists. A website known as Jigoku Ts?shin (Hell Correspondence) may only be accessed at midnight by one who harbors a desire for revenge against their tormenter. Should someone submit the name of one they hate, the Jigoku Sh?jo (Hell Girl) will offer them a black straw doll with a red string wound about its neck. If the string is pulled, she will ferry the recipient of the revenge straightaway to Hell, but on the condition that those who request her intervention fall into Hell as well at the end of their natural lives.
During each story, the protagonists' dramas are explained in detail from the start of their grudges, through the escalation of their torment until it becomes unbearable and they resort to the "Jigoku Ts?shin" (correspondence with Hell) - a mysterious black colored web site only accessible at midnight. The contents of the site are only a text: "????????????? (We will take revenge on your behalf.)", a text box where the grudge's object must be written, and a "?? (Send)" button. Some time after the post, they are visited by Enma Ai, a young red eyed girl wearing a traditional sailor school uniform. She delivers them a black straw doll (In the second season, the doll may also be red or dark blue depending on who turns into it) with a red string tied to its neck, and she tells them that if they want their vengeance to be delivered, they must remove the string from the doll, and their enemies will be immediately taken to Hell. However, a crest shaped mark will appear on the protagonists' chests, always reminding them that after their lives come to an end, they must give compensation by having their own souls also sent to Hell.
Enma Ai lives in a house in an unknown world that is in eternal sunset with her grandmother whose face never appears. Ai is helped by her three assistants. When they are not under her services, they stay in the form of three straw dolls, otherwise they assume the form of Ichimoku Ren, a handsome young man in casual clothes and takes the form of the blue straw doll, Hone-Onna, a beautiful woman wearing a kimono with the obi (sash) tied in front which signifies she is a prostitute and takes the form of the red straw doll; and Wany?d?, an old man wearing a hat and a red scarf and takes the form of the black straw doll. They help her during the event when their victims are confronted with their own sins, prior to the moment when Ai (dressed in traditional kimono with floral patterns) ferries them to hell. Also, the trio helps her investigate the true nature of their clients.
In episode 8 of the series, two recurring characters are introduced: A journalist named Shibata Hajime - a former scandal hunter-blackmailer who turned to investigating the stories involving the Jigoku Sh?jo; and his daughter Tsugumi. After an encounter with Enma Ai, Tsugumi starts to have visions of what Ai sees and thus the two become more and more involved in Ai's matters. Hajime doesn't agree with Ai's methods to deliver vengeance for her clients, and tries to stop those who contacted Jigoku Sh?jo from using her service with Tsugumi's help.
As the series progressed, it was revealed that Hajime and Tsugumi were the descendants of a man named Sentar? Shibata. Sentaro and Ai are childhood friends as well as cousins. The village they lived in had a tradition; Every seven years, a seven-year-old child would be sacrificed to the gods, allowing for seven more years of prosperity. Ai was chosen as the sacrifice, but her parents asked Sentaro to hide Ai rather than leave her to be sacrificed. Sentaro agrees, and takes her up to the mountain, keeping her hidden for six years. However, the village also experiences a great famine.
During one of Ai and Sentar?'s secret meetings, the villagers catch them and bring them to the village, where Ai and Sentar? are accused of angering the Mountain Gods. The villagers throw Ai and her parents in a pit and force Sentar? to bury them as an atonement for hiding Ai. Ai is conscious at the moment and feels betrayed by him.
After Ai was buried, Sentar? awakens one night and went out of his home. When he returns, he sees Ai setting the village on fire. Out of insanity and guilt, Sentar? runs away. He grew up regretting what he had done and builds a temple in remembrance of Ai and other sacrifices to the Mountain Gods. He opens a candy store named Shibataya that sells a black candy that he and his descendants and other owners of the store send to the temple as an offering.
The realization of Hajime and Tsugumi's relation to Sentar? awakes Ai's hatred, and she attempts to kill Hajime and Tsugumi but failes. For doing so, Ai was to be sent to hell, but she escapes and decides to provoke Tsugumi into sending her father to hell by showing Tsugumi how her mother died and her father's denial of his responsibility, Ai keeps pressing Tsugumi to pull the string while Hajime is trapped in Ai's world, but is subsequently able to escape because of Ai's grandmother who releases him for an exchange (whatever the exchange actually was never shown).
Hajime returns to Tsugumi and admits his faults and tells Tsugumi to send him to hell. This angers Tsugumi because she feels that his acceptance of hell infers that he does not value their moments together. She returns the straw doll to Ai, and Ai later incinerates the temple built by Sentar? either as a way of relieving her grudge (in this case, the destruction of the temple would symbolize Sentar?'s release from his regret) or as a sign that she would not forgive Sentar? despite all that he did to show his regret (the destruction of the temple in this case would symbolize the refusal of Sentar?'s apology). The season ends with Hajime and Tsugumi going back to normality and Ai continuing what she has been doing for centuries - sending people to hell.