The story begins with Mizuki receiving yet another confession of love by a guy who won't back down even after Mizuki tells him he's male near a supposed Magic Mirror that grants the wish of anyone who confesses to someone before it. Meanwhile, the Norse god of trickery Loki has decided to turn her eye to the mortal world for a new form of entertainment. Seeing Mizuki's situation, she decides to have some fun and turn Mizuki into an actual girl.
Waking up with two new breasts and one missing willy, Mizuki reveals his situation to Takeru and desperately looks for a way to turn himself back into a boy and hide his new form. Just to add to the problem, Loki has decided to enroll in Mizuki's school to directly provoke and antagonize him.
Boku Girl contains examples of:
- Childhood Friend Romance: Mizuki and Takeru have been best friends since they were kids. After the Gender Bender thing, Takeru begins to feel strongly attracted to Mizuki, but tries to suppress it as much as possible. Mizuki doesn't notice it at first, but later begins to feel attracted to Takeru too.
- Contrived Coincidence: In this case, they're contrived by Loki, usually. For instance, the one time Mizuki is forced to wear womens' panties is also the one time he ends up flashing them to Fujiwara, courtesy a toy with Loki's appearance hooking onto and pulling up the skirt he'd been made to wear at the time.
- Disguised in Drag: Now that he's a girl, Mizuki's boys' uniform counts as a crossdressing disguise.
- Ecchi: The manga doesn't shy away from showing Mizuki's new assets.
- Entertainingly Wrong: Characters who learn Mizuki is female, but not that he was transformed into a girl, usually take Mizuki's declarations that he's a guy as something along the lines of Mizuki being transgender. Another character, Fujiwara, who does know Mizuki was male but sees him doing girly things (such as wearing panties) goes in the opposite direction and assumes Mizuki wants to be a girl.
- Forceful Kiss: In Chapter 17, Takeru just can't hold his confused self back anymore and kisses Mizuki in a heated moment. Mizuki doesn't take it well.
- Gender Bender: Caused by Loki the trickster god.
- Jizzed in My Pants: As a result of a badly placed rope (courtesy of Loki). Not familiar with the sensations, Mizuki thought it was a case of Potty Failure.
- Jumping the Gender Barrier: Mizuki and Takeru have been best buddies since childhood and Mizuki appreciated that Takeru was the only one who treated him as a guy. After Mizuki turns into a girl, Takeru suddenly finds himself strongly attracted to Mizuki, while Mizuki eventually also begins to think of Takeru as more than a friend. Things get really difficult for Takeru after Loki feeds him a dream of a truly female Mizuki. Immediately afterward, Takeru notes that he can't view Mizuki as a guy any longer.
- Locked in a Room: Chapters 39-41 feature Takeru & Mizuki getting locked in the gym storage room immediately after Loki gives Takeru a dream featuring himself in bed with a truly female Mizuki and Mizuki reveals he has a minor issue with claustrophobia and needs some comfort.
- The Modest Orgasm: In chapter 11. It was so modest not even Mizuki fully realized what had happened, thinking instead it was a case of Potty Failure.
- Panty Shot: The one time Mizuki is forced to wear womens' underwear (because his boxers were left out to dry during a rainstorm) is also the one time he ends up flashing his undies to Fujiwara.
- Secret Keeper: Takeru and Mei are the only ones who know Mizuki was transformed into a girl. Yamada knows Mizuki is physically female, but not that he was gender bent. As far as Mizuki knows, the same is true of Loki. As of chapter 38, Fujiwara has also been let in on the full secret.
- Shout-Out: In chapter 6, there is a "Lordgenome" clothing store.
- Stronger Than They Look: Mizuki is pretty small and girly, but he can easily throw people much bigger than him by the arm.
- Tomboy: Fujiwara is a closet tomboy, having loved mechas since she was a child and often behaving more masculine than the manliness-obsessed Mizuki.
- Transsexual: Outsiders who learn Mizuki is a girl seem to make the assumption that Mizuki falls into this trope.
- Triang Relations: Mizuki has a crush on a girl named Fujiwara, who is more interested in Takeru. Meanwhile, Takeru is developing an awkward attraction to Mizuki's new female body.
- Troll: Loki's reason for being and the entire reason she does anything. She likes to cause a mess then sit back and enjoy the show.
- Unresolved Sexual Tension: Mizuki and Takeru, mostly from the latter.