- In the first game, the music used for the battle against Golden Freddy is the final boss music from the PSP Updated Re-release of Riviera: The Promised Land.
- The final sequence of the second game to EarthBound, where Toy Freddy and his party are sent to a cave-like area that may be in the past, and find Balloon Boy first merged with a strange machine and then turns into a bizarre red haze styled like Giygas.
- Also Balloon Boy mentions that the world will have nothing but a desolate hope once he finishes Toy Freddy.
- In the Import Scenario, Balloon Boy literally becomes Sephiroth, complete with a modified version of One Winged Angel in the background.Music: "Estuans interius ira vehementi Estuans interius ira vehementi"Freddy: (Singing over "Sepiroth") "Enragement Child."
- Music from the Persona series sans the Persona 2 duology is regularly used throughout the games, but the third game takes it a step further with Golden Freddy, who is able to summon Shadow Freddy and Shadow Bonnie with an Evoker. "Thou art I..." is used to seal the connection.
- Upon realizing that the office door is locked five times over, Springtrap comments that it isn't just security... It's advanced security.
- The setup of the credits in 2 is a reference to one used in Revolutionary Girl Utena, various mixes of the aforementioned credits' theme song Virtual Star Embryology are used throughout the games, especially in 2 and Zettai Unmei Mokushiroku is used in 3.
- Garry's Mod has been used for a number of cutscenes starting with 2. The use of party hats as Mooks in the first game is a reference to Prop Hunt on the FNAF map in Garry's Mod, where party hats are one of the possible objects.
- "Final Mix" is a reference to the Updated Rereleases of the Kingdom Hearts games.
- In 2 Final Mix, the setup of the final boss (namely, being fought in four phases, with one team of three animatronics in each phase) is a reference to the first part of Sonic Heroes' final boss. Not only that, but "What I'm Made Of" plays during the battle with the Refurbs.
- There's quite a number of tracks from the Sonic series in the games, such as a MIDI remix of The Doomsday Zone filled with Michael Jackson voice clips, one of the minigame songs from the same games with some of the sound channels removed and also filled with more voice clips, the glitchy music in the minigames in 2 are more Sonic 3 tracks corrupted with Vinesauce, the sewer music from Casinopolis and Gamma's theme, and as mentioned above "What I'm Made Of".
- The vents in Act 3 of 3 use Prison Lane and Lost Colony's themes for the Past and Future vents respectively.
- Things from the Mega Man series pop up rather often. Splash Woman is revealed in 2 to be Toy Freddy's ex, and her level's theme along with those of two other Robot Masters' in the same game are the songs used in 3's minigames. Vile, the aforementioned couple's son, shows up in The Stinger of 2 swearing revenge on his father and is the protagonist of the first game's W Scenario.
- In particular, Act 3 of 3 has a direct reference to an infamous scene from Mega Man: Maverick Hunter X — namely, Vile declaring "NO! NOT A CHARGED SHOT!" and then immediately dying from it. In Fuckboy's, after getting Vile's health down, Toy Freddy interrupts the battle by using a charged hat toss, which causes Vile to die (with exactly the same dialogue [[spoiler:minus the word "NO!").]]
- Act 3 of 3 has the "fight" between Freddy and Golden Freddy end with "It was a good experience."
- When Freddy goes to the music store in Act 3, Tomodachi Life's Clothing Shop music plays in the background.
- As Vile chases after Freddy in the futuristic worn-down version of the original pizzeria, the theme from Ao Oni plays.
- According to the third book in the W Scenario, Vile lost his wife to a "kratt racing dinosaur".
- Balloon Boy to Xehanort, appearing in every game as the True Final Boss and in a different form.
- Using the Business Card in Act 3 of 3 leads to a sequence that ends with Freddy singing "All Star". The accompanying picture is Freddy's head 'shopped onto a picture of Shrek.
- The difficulty levels in 2 are Normal, Proud, and Critical, just like Kingdom Hearts.
- And of course, there's the use of a DeLorean for time travel.
Shout Out / Five Nights at Fuckboy's