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- Rena from Higurashi: When They Cry mistook her friends for aliens in "The Atonement" chapter. Of course, she was at best, at lv.4 Hinamizawa Syndrome.
- One episode of Ouran High School Host Club had Honey's younger brother Yasuchika accuse him of being an alien simply because he eats three cakes at once in less than a second once a week.
- Franken Fran helps an actress who has fallen for a male lead who is obsessed with anime features, and wants to star opposite him in live-action adaptations. She insists on ever more extensive surgery but fails to take Fran's advice at the hazards in her rush to bed the actor, and cosmetically falls to pieces. He flees in terror, then goes on so many talk shows raving about Grays trying to abduct him that he doesn't get any more roles.
- A running gag in Shinryaku! Ika Musume - Cindy Campbell and her colleagues are convinced that Ika Musume is from outer space, and they would very much like her to visit their laboratory.
- The Teenage Mutant Ninja Turtles do this on purpose in the third Mirage comics volume; aliens having openly made contact with Earth, it's apparently easier for people to accept that than homemade mutant freaks.
- Cracked had a 3rd Rock from the Sun parody in which aliens mistake the disguised alien family for real humans.
- In Back to the Future, the DeLorean Time Machine was mistaken for a UFO in 1955 due to its gull-wing doors. The fact that Marty was wearing a radiation suit at the time didn't help.
- He turns it to his advantage later, when he orders his father to hook up with his mother.
- Grand Fenwick's chainmail-clad longbowmen successfully invade 1950s New York City in The Mouse That Roared because of being mistaken for Martians.
- Played for Laughs in The Avengers (2012) where Bruce Banner as the Hulk falls on a warehouse, half-destroys it and becomes human again. There, he speaks to an old man, a security guard, who believes Bruce is some sort of alien. The security guard is played by Harry Dean Stanton, who was in Alien.
- In the Super Mario Bros. movie, when Mario and Luigi are escaping from the police force, a news report identifies them as "alien plumbers".
Luigi: Aliens? We've gotta deal with aliens too?Mario: Luigi, we're the aliens!Luigi: We are? Cool!
- This scene from Eraser.
- In Big Game, the first question Oskari asks Moore is what planet he's from, and the second is whether he comes in peace. While the escape pod does look like a space capsule, it has big USAF written on it, which should tip the kid off.
- In Spider Robinson's The Free Lunch, when the protagonists notice that there's something very odd about some of the attendees at the theme park where they live, their initial deduction is aliens. This being Spider Robinson, however, they're actually time travellers.
- Take Me to Your President by Leonard Wibberley was about a fellow nicknamed "A-1" from a small British town called Mars, who accidentally got loaded into an experimental rocket. When it landed somewhere other than it was expected to, and he came out wearing the space suit he'd found and saying he was from Mars, well....
- In Amy Thomson's The Color Of Distance has the protagonist, Dr. Juna Saari, spend five years among the alien Tendu, who give her a moist color-changing skin and internal linings that keep her hair from growing and help with the planet's aversion to No Biochemical Barriers. When humanity comes back to pick her up, the first contact is with a suited man who thinks she's one of the Tendu, and she plays along for a bit before saying "I believe the line is 'Dr. Livingston, I presume?'"
- Christine Peacock sees mysterious lights in a field near the vicarage in Aunt Dimity Digs In, and she's convinced she saw aliens land there. She's even more convinced when a circle of trampled-down grass is found on the spot the next morning. In fact, Sally Pyne and one of the archaeology students were exercising there at night, mostly because Sally was embarrassed to be seen exercising.
- A long-running plot point of Animorphs. The Yeerks thought the kids were Andalites.
- Weirdly inverted in 1895 science fiction novel Journey to MarsFull Title by Gustavus W. Pope. When the protagonist sees Martians for the first time, he mistakes them for inhabitants of the land inside the earth's core (note that the existence of such a land was still considered possible by scientists at the time of writing, and the concept of extraterrestrials was still relatively obscure even in fiction).
- Depending on your definition of "another world", the fact Rincewind twice (Eric and The Last Continent) appears in a summoning circle and is therefore assumed to be a demon probably counts.
- In the Doctor Who New Adventures novel Death and Diplomacy, Bernice Summerfield, in an alien culture which has a wide range of races but no known contact with Earth, meets a guy who looks completely humanoid but, to an experienced traveller like her, his body language and so on is clearly off. This is her future husband Jason Kane, who plays along for a while before making some sarcastic comments about being patronising to the natives.
- "Tomorrow is Yesterday" from Star Trek: The Original Series.
- The I Dream of Jeannie episode "U-F-Oh Jeannie", where Tony was mistaken for a Martian by a group of rednecks in the Deep South.
- In Kyle XY, Josh Trager claims, half-jokingly, that Kyle is an alien. (In fact he's an experimental clone with psychic powers.) Two years later, when Kyle finally reveals his history to the Tragers, he comments that Josh's guess may have been the closest to the truth.
- In the Lost in Space episode "Visit to a Hostile Planet", the Robinsons go back through time to 1947 and are mistaken for aliens when they land on Earth.
- In The Addams Family, the Addams are mistaken for aliens by the military, who approach them claiming to wish peace and asking them lots of questions. As a consequence, The Addams believe the army men are aliens as well (because of their green wardrobe).
- SG-1 deliberately invokes this when they're stranded in 1969, presumably figuring that it's a quicker explanation than the actual one.
- Averted in the TV Show, Community. Abed plans to 'mess with' Troy by using the classic sitcom set up for this, except that he didn't fool Troy for a second.
- Done in the Torchwood episode "Countrycide", where the team thinks that some aliens are responsible for disappearances and attacks. Turns out, it's a bunch of humanitarians.
- During the episode "Mush-Rumors" of The Adventures of Super Mario Bros. 3, a human family ends up driving into the Mushroom Kingdom by accident and are called aliens by one of the Toads, which then gets spread and exaggerated to the point where Bowser thinks they're an alien invasion force in disguise. The fact that they look not-unlike the human Mario and Luigi never comes up.
- There's a Simpsons episode (The X-Files crossover) where Mr. Burns is mistaken for an alien from the results of the various dubious medical treatments he undergoes and glowing green in the dark, a side effect of working at the nuclear power plant.
- Spongebob Squarepants had an episode with them using Sandy's rocket to land "on the moon" (actually they circle around the moon and land back in Bikini Bottom) and go to hunt "moon clone aliens" which look exactly like their friends on earth.
- An episode of The Mask animated series featured a government agent and a scientist mistaking The Mask for a hostile alien due to a series of coincidences (not that it's hard to mistake him as such in the first place...)
Agent: Hmm...Subject has green skin. Imagine! Just like in the funny papers!
- Inverted and played straight in one episode of Viva Piņata. Fergie Fudgehog is conned onto going onto a defective rocket ship that crashes. When he comes out, his foggy helmet makes his friends look like aliens to him, and it makes him look like an alien to his friends! Needless to say, Hilarity Ensues.
- The Hey Arnold! Halloween episode. Also doubles as a Parody Episode due to all the Orson Welles references.
- In The Santa Claus Brothers, one of the elves is mistaken for an alien.
- In one episode of Class of 3000, Phily Phil is mistaken for an alien by an incompetent MIB-style agency when he crashes a spaceship he invented.
- In the South Park episode "Starvin' Marvin in Space", the people of Australia thought Marvin was an alien. To be fair, he did emerge from a spaceship.
- An episode of Gargoyles has an actual alien think the title characters are also aliens.
- Invader Zim has an unfinished episode where Zim tricks Dib into thinking Poonchy, Drinker of Hate was an Irken invader. Hilarity Ensues.
- Phineas and Ferb, "Invasion of the Ferb Snatchers": A series of unlikely coincidences cause Candace to believe that Ferb is an alien. She's obviously wrong, but Phineas and Ferb are helping an alien rebuild his spaceship.
- Rocko's Modern Life has "The High-Five of Doom", where Rocko and Heffer think Filbert is an alien after reading his diary. It was All Just a Dream, but they were still freaked out.
- Rugrats did this several times:
- In "Aunt Miriam", Tommy and Chuckie become convinced that Tommy's Great-Aunt Miriam is an actual ant-monster from outer space.
- In "The Alien", Angelica couldn't fit into Chuckie's new playhouse and, out of spite, she tries to convince his friends that Chuckie is an alien and the playhouse is a spaceship in disguise.
- The Goof Troop episode "Close Encounters of the Weird Mime" had Goofy's attempts at taking up mime and Max and PJ's attempt at making a home sci-fi movie collide hilariously when the boys accidentally broadcast their video of aliens threatening the Earth.
- One episode of The Flintstones has Fred and Barney trying to help a pop-music group that has an "alien" gimmick get to the concert, at the same time that the radio announcer uses an overly-cryptic ad warning people "The Way-Outs are coming!" in a War of the Worlds-style fashion, and this makes the rest of Bedrock pull out the Torches and Pitchforks.
- In the Dexter's Laboratory episode "Smells Like Victory", an experiment gone wrong leaves Dexter's lab all smelly and dirty, which leads to a paranoid general mistaking it for a ground base for "evil filthy aliens". Meanwhile, Dexter is convinced by a garbled transmission that the safety-mask-wearing soldiers busting into his lab are the evil filthy aliens.
- After Yuri Gagarin became the first human to enter space and return successfully, a woman who saw his capsule land asked him "Can it be that you have come from outer space?" He replied "As a matter of fact, I have!"
- Most likely apocryphal, since it's now known that he actually bailed out of his capsule, and wouldn't have landed near it.
- Similarly, when John Glenn was orbiting in the Friendship 7 in 1962, the mission planners weren't exactly sure where the capsule would land - somewhere near Australia, as in any part of Australia or the surrounding oceans or islands for a pretty far distance. Glenn was worried what the aboriginal Australians might think when seeing a man in silver emerge from something that fell from the sky so he took a short speech with him rendered phonetically: "I am a stranger. I come in peace. Take me to your leader, and there will be a massive reward for you in eternity."
- Allegedly happened to an SAS troop doing a training exercise involving a High Altitude Low Opening parachute jump. Having landed in the middle of nowhere in the middle of the night, they walked up to the nearest farmhouse to get directions. A woman opened the door and found herself facing several tall beings dressed head-to-toe in black including oxygen masks and blinking formation lights.
Troop leader: "Excuse me, ma'am. Can you tell us where we are?"Woman: "Earth!" (slams door in their faces)