- When the show manages to slip in a funny moment, it stands out all the more. An example? Well, the episode where Hiroto barricades himself into a classroom, and Kiyome recalls a similar occasion... where Maya's sister Yumiko climbed up the lighthouse and announced to the whole island that she would become an idol singer!
Maya: Hey, sis, did you really do all that?Yumiko(sweating bullets, with a Luminescent Blush): AAAAGH! STOP TALKING ABOUT IT!
- Combines with Crowning Moment of Awesome and Crowning Moment of Heartwarming. At Chizuru's trial, all the pilots stand together to confessed that they all took part in altering Maya's data. Soushi gave a lengthy speech why he is against Maya piloting, Mamoru and Sakura gave a reasonable explanation, and Kenji said that he accidentally changed Maya's data because he wanted to changed his in the first place due to being scared of piloting a Fafner, earning a facepalm from his mother and a boot to the head. And Sakura catches the boot.
- Mamoru's parents are actually complimenting him, earning a "What the hell" from Yoko.
- When Kazuki is asked about his reason, his reply is that he has no special reason (except that he doesn't want Maya to fight), which earned a facepalm from his father.
- Mizoguchi even joins in and say he accidentally altered the data when he was looking for Maya's measurements, which earned him a "Shut Up" from the committee (And a continued facepalm from Fumihiko). And the fact that he was asked to testify from the audience seat because it was too troublesome for him to come around to the defendant's stand. Oh, and he's going to read that out loud if he's not told to shut up.
- When Tsubaki takes the stand, everyone's reaction was "This is like bringing God to the court!"
- Finding out that Soushi is extremely socially awkward outside of the Siegfried System can come across as this.
- The convenient-eleven-steps-from-his-room vending machine comes to mind.
- The sento sequence is a large one, but it really takes the cake when the girls harassing Canon on the opposite side, the male cast are certainly enjoying it......Except Kazuki and Soushi, who just exchange a few words in deadpan.
- Combines with Crowning Moment of Awesome. Even this series has one, in the finale after Kazuki and the Mark Sein had been absorbed into the Festum world and it looks like he might get out of it, the Mark Nicht with Idun appears in the real world proclaiming "I'm still here!". Only to be covered in crystals and assimilated by the Sein and Kazuki. Those who hated Idun this comes off as both awesome and funny.
- Maya finds out that she has a half-brother who is a member of the Human Army, and confides to Canon about it. Due to not supplying the context, Canon misunderstands and thinks Chizuru and Fumihiko got busy.
- When explaining each characteristics of the three new pilots, at the end of each pilot's description, Sakura gives a note in Layman terms, by comparing them to Kazuki, except Sui, which was compared to Soushi.
- When Canon tries to explain the characteristics of the Fafners (Which is repeated once in the original series, OVA and movie), Sui keeps cutting her and completing her sentence. He is ultimately stopped by the combine elbowing of Leo and Mimika.
- The character duet Taiyou to Tsuki that was released with the second DVD/BD of Exodus is so upbeat and happy sounding that it took almost everyone by surprise. And then you read the lyrics and it's hard not to laugh. Are we sure this song is related to Fafner?
- Reactions from Kohei Kiyasu (Soushi's VA) in various interviews about this song are downright funny.
- Rina, who is taking a bath, suddenly disappears and appears on Sui's bed. Cue Freak Out in sync. Although in this case it's not something to laugh at.