- One of the show's downright funniest scenes occurs episode 12. Fakir, after falling into a large trench with Ahiru/Duck, becomes heavily embarrassed and thus flustered when he learns Ahiru is actually "the" duck he consoled with while crying in episode 10. Since Fakir is usually as guarded as Fort Knox, this makes it five times funnier. The fact that Ahiru suddenly turns into a girl again and doesn't consider her nude status in front of Fakir until too late makes the scene only that much more hilarious.
- When Fakir opens a door and pretty much every girl in the school falls in.
- Ahiru flailing over Mytho in early episodes, made funnier by his nonchalant reactions.
- Duck!Ahiru, plus Uzura, plus Fakir, plus water.
- When Ahiru is "rescued" by Fakir in the boy's locker room.
- Anytime Ahiru's friends Pike and Lilie try to help her in her lovelife.
- When Ahiru tries to confess that she is Princess Tutu to Mytho, Fakir intervenes and shouts, "PRINCESS TUTU." Ahiru quacks and turns into a duck, cue Fakir pushing Mytho to the side and saying this,
Fakir: "I saw her flying, over there, in the sky. But then again, it may have been a crocodile."
- "I will have you MAAAAAAAAAARRY MEEEEE!"
- Any scene with Femio in it. Period. No wonder he's an Ensemble Darkhorse/One-Episode Wonder.
- In Akt 20, an outtake accidentally left in the dub results in Fakir randomly saying he's going to write a letter to the President while staring at a paper and pen.
- Fakir first finds out Ahiru is a duck. But wait! She's not just any duck, she's the one Fakir hugged. Cue Luminescent Blush and the first Please Put Some Clothes On moment.
- Drosselmeyer, being the kooky man he is, gets a few, most notably when Rue after having taken Mytho makes a comment aimed at Drosselmeyer, who replies "Huh what? Who said!?," in utter shock.
- The first line in the series.
Narrator: Once upon a time, there was a man who died.
- Not all that funny in and of itself, but the first line of the series was also the very first line in JesuOtaku's review. The second line is JesuOtaku commenting, "That was a short story, wasn't it?"
- When Ahiru and the others find their happy ending, Drosselmeyer is leaning forward in his rocking chair so dumbfounded, he, chair and all, come forward slamming his face into the gear below.
- The bloopers themselves are quite funny with special mention going to "Travolta back in the day" and "Never touch the Mytho."