Haruhi Fujioka, scholarship student, is immediately mistaken for a boy when she arrives at elite private school Ouran Academy. Searching for a quiet place to study, she stumbles across the Host Club, and, in an attempt to escape, accidentally breaks a ¥8 million vase. To pay back the debt, Haruhi becomes a member—needing to be "requested" by at least one hundred customers before she can leave. However, one by one the Host Club members discover her true gender; all except Tamaki, who accidentally sees her in her underwear before he gets the hint.

The Host Club finds out that one of their regular customers, one of the few that skips from host to host regularly, is having trouble with her fiancé. The group then cooks up a plan to help, involving a dance, a kiss, and a big spotlight. Unfortunately, in the process, Haruhi has her first kiss; but not with the fiancé, but with the fiancée.

The time has come for the school's physical examinations, so the club must find a way to protect Haruhi's Big Secret. Their attempts fail miserably until Kyoya steps in, with a doctor who promises not to reveal her secret. Meanwhile, someone accused of attempting to "make a pass" on one of the female students, Dr Yabu (literally, Quack Doctor) is actually searching for his daughter after she and her mother left him due to financial problems. Kyoya points out that, if the man's family is really that poor, the girl would be attending Ouran Public High, rather than the prestigious and very expensive Ouran Academy. Tamaki gives him directions, explaining that, even though he might get hurt later, it's up to him to find the truth.

Renge, an intense young woman obsessed with dating sims, declares herself the Host Club’s new manager! Her first order of business: give each of the Hosts a "dark side."

The twins beg to be allowed to visit Haruhi's home, but she refuses. Haruhi comments about the differences between Hikaru and Kaoru, which triggers a fight between the inseparable siblings, even making them dye their hair different colors, blue and pink, in order to be told apart. When Haruhi finally stands up to their fighting, saying "if they've never fought before, they might need help stopping," Kaoru is about to give Hikaru a cursed doll with his name written on the back - but when Haruhi steps in, he gives it to her instead. However, when she turns it over, the back says "Fail," - alerting the host club it was all a trick to be allowed to visit Haruhi's house.

The Host Club visits the "real beach" in Okinawa upon Haruhi's request, but, Kyoya having invited customers, Haruhi is still unable to wear a swimsuit - much to the others disappointment. The twins devise a game to see who can find out what Haruhi is afraid of first, drawing Tamaki in with the explanation that only close friends show each other their weaknesses. Kyoya hypes up the competition by offering up photos of Haruhi in middle school. One accident occurred that caused a fight between the Host Club members. Kyouya, however, made Haruhi realize what her mistakes were and she eventually apologized for her wrongdoings. Tamaki wins secretly in the end, during a thunderstorm. However, the rest of the host club walks in at the most inopportune moment, as he covers her ears and places a blindfold on her to "block the thunder." The group ends up leaving with Tamaki chasing after them, trying in vain to convince them that he's not a pervert.

When the son of a gangster, Ritsu Kasanoda, seeks Mori for tips on how to change his scary image and gain friends, the Host Club immediately jumps at the opportunity to change his image, making many humorous results of their efforts. The members of the Host Club also frequently call him Casanova and bossa nova. However, Ritsu ends up discovering Haruhi's secret.

After Ritsu walks in on Haruhi changing, he later joins the Host Club, but as a customer. When he insists on Haruhi as his host, the other hosts get nervous and the clients get excited. Tamaki starts to realize his feelings for Haruhi, and Ritsu nearly goes insane, while Haruhi remains blissfully oblivious.

The Host Club participates in the annual school festival. Tamaki's father and grandmother turn up there. However, the arrival of Eclair Tonnerre, a woman who Tamaki was told to take care of by his grandmother, brings an unforeseen turn of events. Haruhi also learns of Tamaki's history, and his entrance into the Suoh family.