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.

An elementary school brat, Shiro Takaoji, seeks help from the Host Club's King to win the heart of women, but what he doesn't say makes all the difference in how much help he gets. He attempts to run away, calling Tamaki a "fake king", and Tamaki and the others infiltrate the elementary school, discovering that Shiro has a crush on a girl who would soon be moving away. Tamaki explains to him he didn't wish to please women, but only to please one woman - the girl he has a crush on. He had joined the Classical Music Club to make her happy and play the piano with her. Shiro learns his part of the piano duet he was supposed to have played with her, and the host club ends up allowing him and the girl to have a small concert in the host club lounge. The episode ends with Shiro entertaining at the host club, warning the clients not to tell his girlfriend; she'll get jealous if she hears he's hanging out with such beautiful women.

The Host Club drags Haruhi to an artificial tropical beach, but an accident separates Honey from the rest of the gang. Mori and Haruhi separate from the rest of the group to look for him, Mori eventually carrying her due to her slowness and clumsiness. Haruhi wonders aloud about Mori's and Honey's relationship, and then twins explain that they are in fact cousins by marriage. Meanwhile, Kyouya's guards, called in to look for Honey, end up mistaking Haruhi as the "small boy" Kyouya had described, and, under his orders, attempt to arrest any "suspicious people", as they believe that Mori looks suitably suspicious. Honey swings in on a vine, amazing Haruhi with his martial arts ability. The gang returns, ending the episode with Haruhi noting, much to the surprise of the twins and Tamaki, that she would enjoy visiting a real beach.

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.

St. Lobelia Girl's Academy's Benio Amakusa, head of the Zuka Club, chances upon Haruhi and, instantly recognizing that she is a girl, tries to convince her to join her school and her club. Convinced that Haruhi will leave them, the boys dress up as girls to show Haruhi that she "can have big brothers AND big sisters - all in one!" Haruhi reveals that she came to Ouran for a reason, and says that she was never planning to leave for Lobelia in the first place.

Interested in the unknown ways of a "commoner's lifestyle", the Host Club makes an unannounced appearance at Haruhi's house to meet her family and see how she lives. Tamaki realizes how independent Haruhi is and some of the reasons why.

Tamaki enlists the help of Renge in teaching Nekozawa to become the princely figure his little sister is convinced he is and help him face his fear of light, eventually leading to him saving his sister from a large, unfriendly cat, leading her to be convinced of his bravery despite the wig and cloak that he wears.

Honey gets his first cavity, and the number one rule until the cavity is fixed is no sweets. He then takes his frustration out on Mori, who is being strict on Honey, but Honey realizes that Mori was punishing himself for not telling Honey to brush his teeth twice.

Haruhi's dream about the day of her admission into Ouran High School becomes a trippy Alice in Wonderland-esque fantasy. Her friends try to tell Haruhi something important, but she only realizes it when in court. At the end of the dream, she meets her mom, who tells her to "enjoy a dream like student life." She wakes up with tears in her eyes, and sees the club dressed up in costumes that look like the ones they wore in her dream.

The ailing Newspaper Club wants to obtain an interview with the popular Host Club in order to save it from being disbanded due to the lack of public interest. Or so it seems. The newspaper club tell lies in their papers, so the club leader wants to interview the host club because he thinks that Tamaki is using his parents' power to control the popular students, and wants to tell the whole school that. Apparently he thinks of Tamaki as his mortal enemy.

During summer vacation, Haruhi gets a part-time job in a pension at Karuizawa. She feels guilty at first for not saying anything to the rest of the Host Club, until they drop in unannounced. A contest erupts when they realize there is only one remaining room at the pension. Hikaru and Kaoru win by using their brotherly love act. When Haruhi's middle school friend visits, things take a turn for the worst.

Hikaru gets jealous of Haruhi's former classmate while at the pension. Kaoru pretends to be sick for the date, and instead sets up a date for Hikaru and Haruhi to try to get Hikaru to think of other people which Tamaki does not take too well. During their date, Hikaru runs off somewhere, and a thunderstorm occurs. Worried about Haruhi, Tamaki calls Hikaru, and tells him that Haruhi is afraid of thunder, letting everyone know Haruhi's weakness. In the end, Hikaru apologizes to Haruhi, who is hiding under a table in a church, during the thunderstorm and comforts her while she is crying. He apologizes for the way he acted, but Haruhi thinks he is Kaoru.

Kyoya, half-asleep, is dragged into a commoner's department store by Tamaki and the rest of the boys, who aim to study the life of ordinary people, and therefore understand more about Haruhi - or play. Kyoya ends up meeting Haruhi there, alone, and they find it interesting how each other views their lives. Towards the end, Tamaki makes a call for a "lost child", who turns out to be Kyoya, which makes Kyoya even angrier at Tamaki than he already is.

Honey has a younger brother Yasuchika, but he has a huge grudge against his sibling. It turns out the reason for his brother's grudge is that Honey eats too many cakes, causing Yasuchika to freak out.

The girls from St. Lobelia's Zuka Club finally manage to rope Haruhi into their academy, and it is up to the Host Club boys and Ranka to save her from Benio Amakusa stealing her first kiss - until Kyouya reminds them of Haruhi's real first kiss in a previous episode. The episode ends with the Lobelia's Zuka Club chasing Haruhi around the stage, attempting to steal her second kiss.

A prequel that tells the story of how the twins were convinced to help form the club, including the "Which One is Hikaru?" game that they always played, including their past with the maid who led them to believe that no one would ever be able to tell them apart, and the cruel trick that they played on a girl in middle school.

Haruhi's class has a Halloween event - The Halloween Special Fear Trial Tournament- in which groups do their best to scare the living daylights out of each other! The class rep isn't so keen on this idea, though, and enlists Haruhi to help him. Kaoru, meanwhile, contemplates a sad truth. Nekozawa decides to scare the group of Haruhi, Kaoru, Hikaru, and the class rep.

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.