- Awesome Music: The opening theme of the English version is insanely awesome for a Biblically-based Anime series.
- "Funny Aneurysm" Moment: One episode has An Aesop in the end, showing Judas as a valued apostle, and how friendly he was with the rest of them. But when you think of how things turned out with him...
- Nightmare Fuel: Episode 5, "Speak of the Devil". Satan has a little fun with the kids at the same time he tries to tempt Jesus. Somehow they all got better.
- The beginning of Episode 14, "Back from the Grave", has Professor Bumble finally return the group home to the 20th century, exactly where and when they left during the storm. At first, all is great; the kids excited and ready to come home to their families. But when Justin runs to his house, he realizes that it's gone (his swing-set only remaining) and that the landscape around him is completely different. He then walks through a grassy knoll to find a marble stone, which later turns out to be his gravestone. Yikes! Justin then meets up with Angie and Corky where they learn of the same thing. Immediately figuring out that Prof. Bumble goofed and sent the flying house to the far future, they try to go back to him, but end up knocking down a locked door, suddenly growing white hair and beards. Wow. Turns out that it was All Just a Dream by Justin. A horrible dream.
- Episode 22 "Judgement Day" has a rather disturbing depiction of Hell despite the super deformed art style in the parable of the rich man and Lazarus.
- Quietly Performing Sister Show: While its sister series Superbook is beloved around the world and has been dubbed into dozens of languages, Flying House seems to be less well known, although it was also popular in its day in Japan. Part of the reason for this may be the content. How many other children's series aired in the United States during the '80s feature beheadings (albeit not depicted on screen), attempted suicides, and demonic possession? Especially a show with a Christian religious subtext. Superbook was never that dark.
- Tear Jerker: Almost every episode has at least one.
- Just the clear fact that three kids from the 20th century end up in a house during a summer storm built by an eccentric professor that just so happens to travel back to Biblical times, hundreds of years from their time, and away from their families. You can't feel sorry enough for them that they are so far away from their parents for so long.
- Episode 15, "Real Treasure". Poor Zacchaeus.
- The entirety of Episode 41: "Golgotha". The kids and SIR (and the viewers) watch helplessly in horror, sorrow and tears as Jesus is ordered by the Roman Empire to carry his cross to the titular site to be crucified. Their bouts of tears of watching the man they literally watched grow up with them walk to his end, along with the Son of Man's heart-wrenching cries to the Holy Father, and even Professor Bumble's anguish from knowing of the story beforehand and the kids' firsthand account of his death (even calling the time machine—something he's bragged about and defended the entire series an "idiot machine")—among others—makes this episode the series' most heartbreaking and tear-jerking episode. You knew it was coming, and it still hits you hard.
- Toy Ship: Implied in canon between Justin and Angie.
YMMV / Flying House