- At the very beginning, when Pinkie is defining "nervicited", the transformation sound effect from Transformers is used as she uncurls from the ball. Her unfolding moves, while appearing awkward for a pony, resemble the transformation sequences of the Transformers as well.
- The way Fluttershy introduces Twilight to the various high school cliques in the cafeteria is similar to the scene in Mean Girls.
- Sunset Shimmer dismissively refers to Twilight and Spike as "Princess Celestia's prized student [...] and your little dog, too!" Also doubles as a Whole Plot Reference, since the story involves Twilight leaving her mundane existence by going through a rainbow vortex to a strange new world with people who resemble her friends and a wicked ruler with diminutive henchmen. When Sunset orders Snips and Snails to follow Twilight, she says, "Bring me something I can use." Meghan McCarthy even said that she envisioned the movie as The Wizard of Oz in reverse.
- One of the related videos on the YouTube clone when the Crusaders are checking their video's comments is from Pound Puppies.
- When the Humane Six start cleaning up the gym, Twilight tosses out brooms, which the other five catch — except for Fluttershy who winces and turns her back, letting the broom hit her instead. Jayson Thiessen confirmed this as a shout-out to a similar scene from Arrested Development.
- The aforementioned Sadistic Choice is very similar to the one Tachyon gave Ratchet in "Tools of Destruction", both being offered to go to their true home and refusing because they know said home can protect themselves but if they leave there will be no one to stop the villain.
- The beginning of the "Helping Twilight Win the Crown" number, with students banging on the cafeteria tables, may be a reference to this Cold Open from Cheers where the bar patrons start singing "We Will Rock You" the same way.
- The Mane Six's transformations are very reminiscent of Sailor Moon.
- During two of the dance scenes, the first when the human CMC dance and in the final dance scene when Twilight and Flash dance, one of the background characters is doing the Gangnam Style dance.
- The way the bolt of magic zaps through the crowd of mind-controlled teens is a reference to the Ark of the Covenant striking the assembled Nazis in Raiders of the Lost Ark.
- During the first dance scene, Sweetie Belle can be seen doing the same dance as Tsukasa from the opening of Lucky Star.
- Two people who look similar to Tsubomi and Erika from Heart Catch Pretty Cure appear multiple times in the film. The Tsubomi lookalike can be clearly seen in the scene where Sunset Shimmer is about to tell Luna about how the gym got messed up. Then, the same character appears with the Erika lookalike in the cleaning-the-gym musical number.
- Derpy's dance with a muffin in the end credits somewhat resembles how the person in Dumb Ways to Die who sold their kidneys danced.
- Demon Sunset Shimmer isn't the only demon to call high school pathetic.
- One of the hairstyles Pinkie Pie tries on for the dance is styled like a swan — much like Queen Uberta styles hers for the wedding in The Swan Princess.
Shout Out / My Little Pony: Equestria Girls (2013)