Danny Phantom: Danny's sister Jazz found out his secret halfway into the first season, and decided not to confront him about it because she believed that Danny would tell her when he was ready. In the meantime, she would help cover for his actions from their parents and teachers by backing up his excuses, to his mild confusion, as well as lines like "You go... somewhere I can't see you and get help!" Danny eventually realizes she knows in Season 2, when she sends him a message through time via the Ghost Zone. She becomes a Sixth Ranger from that point forwards, albeit to the initial annoyance of the others due to her overexuberance over finally being included.
Bruce Wayne figured out Batgirl was Barbara Gordon at an indeterminate point, but didn't tell her until revealing his own identity. That he also kept this a secret from Dick Grayson was the last straw that convinced Dick to leave Batman and become Nightwing.
Barbara also later attempts to come out as Batgirl to her father, Commissioner Gordon. Before she can state it outright, he heavily implies that he already knows, is proud of her, and doesn't want to "officially" know.
Superman: The Animated Series: Lana Lang surprised Superman by revealing that she knew who he was. It helps that in the Superhero Origin premiere, they are childhood friends and Clark confided in her about the weird things that were happening to him as his powers began activating, and then she saw him save a family from a burning van without getting so much as a blister. Honestly, it would be surprising if she didn't connect the dots between "superpowered childhood friend" to "new superhero in the city said friend just moved to".
Implied in "Unmasked". When Terry unmasks himself to reassure a kid he's rescuing, Cobra later tracks the kid down and checks his memories for Batman's true identity. The resulting image is Batman with the head of the kid's action figure, which Terry takes to mean that the kid didn't see his face well and subconsciously replaced the image. As proof, he walks over to the kid's soccer game and mentions to Maxine that he sees the kid everyday, and he hasn't figured it out. The last shot, however, is the kid looking back and giving a knowing smile, implying that he does know but kept it secret.
It's been revealed in the comic adaptation that Dana Tan knew about Terry being Batman before he revealed it.
Word of God indicated that Bruce knew for a long time that Terry is his genetic son long before Terry figured it out for himself.
In the early episodes, it was implied that Barbara Gordon already knew that Terry was the new Batman before finally acknowledging it by meeting with Bruce in the Batcave. (Of course, he's the obvious suspect for anyone who knows that Bruce was the original Batman.)
Virgil's dad Robert in Static Shock only consciously invokes the trope in the interim between his capture by the villains and his first conversation with Static, as it's then that he reveals that he knows the truth. (There aren't many reasons to kidnap a middle-aged counselor and sometimes community leader as leverage against a superhero.) Cue the page quote.
In "Starcrossed", events transpire which require the members of the League who have civilian identities to reveal them to one another. The Flash hems and haws, until Batman, like it ain't no thang, shows why even in the TV-PG world of JL he's still the gosh-darn Batman:
Flash: Hold on, what about the whole "secret identity" thing? I mean, I trust you guys, but I'm not sure I'm ready to... Batman:[jabs a finger in Flash's chest] Wally West... [jerks a thumb at Superman] Clark Kent... [pulls off his own mask] Bruce Wayne. Flash: Show-off.
In the Unlimited episode "Ultimatum", Amanda Waller reveals that she's always known Batman's identity when she angrily calls him "rich boy".
DC Super Hero Girls (2019): The episode "#BreakingNews" has Lois Lane set out to discover the identities of the titular hero team, and within the span of a scene transition, she's essentially figured them out already. Jess (aka Green Lantern) tips the rest of the girls off, so they do their best to put her off the trail, only for their Bad "Bad Acting" to serve as confirmation. However, Lois decides not to submit her story to the news after dwelling on the matter and realizing the harm it could cause them, keeping her knowledge to herself. Of course, she doesn't tell our heroines this, so they end the episode believing that she didn't run the story because they successfully tricked her.
Glitch Techs: Miko's younger sister Lexi serves as this, having witnessed their parents get system restored in the first episode and keeping records some of her sister's Glitch Tech activity since then. Miko regularly allowing her Chocobo-expy Ally to wander their shared bedroom and being a terrible liar who keeps alluding to her real job probably didn't help. She becomes a regular Secret-Keeper in episode nine, when she uses her knowledge as blackmail to get Miko's help.
Several episodes of He-Man and the Masters of the Universe (1983) hint at He-Man's mother, Queen Marlena, knowing Prince Adam is He-Man but she never quite comes out and says it. On at least two occasions she has deliberately put her son in a position where he can help people as He-Man.
Prince Adam: I was wondering, when Skeletor had us all chained up, why did you free me instead of one of the others? Queen Marlena: Because you are my son, Adam. I didn't have time to free everyone. And I had a... feeling you would know what to do. Prince Adam: Mother, ah... Queen Marlena: Adam, a mother always knows her own son. And what he is capable of doing.
In Hey Arnold!, Brainy stalks Helga whenever she goes, and thus knows all of her secrets. However, Helga doesn't seem to realize it, despite talking openly about her secret love in front of him. Nevertheless, Helga keeps punching him in the face. Running Gag much? It's been implied once or twice that he may or may not think she's actually talking about him.
In Invincible (2021), towards the end of the first season, Mark reveals that he's Invincible to Amber, hoping that it would fix their rapidly deteriorating relationship, or at least begin fixing things between them. It doesn't work. She figured it out a long time ago and admits that she felt offended by him constantly lying about his activities instead of telling her the truth. Mark using the reveal as a final gambit only serves to annoy Amber even more, so she dumps him regardless. Likewise, in the season finale, they quickly piece together that Omni-Man is his father.
In the Grand Finale of Littlest Pet Shop (2012), Blythe's father Roger reveals that he knew of her ability to talk to animals since day one, because her mom had the same power. He was just waiting until she was comfortable with telling him herself.
Mega Man: Fully Charged: As far as Aki and Suna are concerned, their father Dr. Light is completely unaware that the former moonlights as the superhero Mega Man. However, it turns out towards the end of the first season that he's been aware the entire time.
In "Cat Blanc", Adrien catches Ladybug leaving his room after dropping off a present from Marinette, and manages to put two and two together. However, as Ladybug forebade the two of them from knowing each other's identities, he can't exactly admit that he knows, so he decides to just pretend that he's suddenly fallen in love with Marinette (which is just fine by her). Of course, this event causes a chain reaction that results in the destruction of Paris and the deaths of everyone in it save Adrien/Cat Blanc himself, and has to be undone with time travel, so by the end of the episode he no longer knows/never finds out in the first place.
In "Wishmaker", Luka finds out Ladybug and Cat Noir's secret identities thanks to the titular villain's power. However, because he used his Second Chance ability as Viperion to keep them from being revealed to Shadow Moth (and everyone else in Paris), neither Marinette nor Adrien remembers being unmasked. However, the fact that he used Second Chance in the first place causes Ladybug to suspect that one or both of them were unmasked, and asks Luka about it after taking back his Miraculous, but he lies and tells her that neither of them were. In "Ephemeral", Ladybug is forced to send Luka a message that would make no sense if Luka did not know Marinette was Ladybug, so she may have picked up on the deception, but most of the events of that episode were time-reversed themselves. In "Migration", he rejects an attempt to akumatize him, but the brief glimpse into his mind allows Monarch to find out that he knows Ladybug and Cat Noir's identities (though not the identities themselves), forcing him to come clean and upgrade himself to Secret-Keeper while also putting himself on a bus so that he's out of Monarch's reach.
Miraculous World: Tokyo TV-special:
Kagami learned that her old friends in Japan are Stellar Force since they use their group chat to discuss their superhero activities. They just forgot to kick Kagami out of it. Primarily because they forgot she was even in it, since she had never sent a single message.
It's strongly implied that Miki managed to deduce that Marinette is Ladybug, which would make her aware of Marinette's secret without Marinette knowing she knows.
Zick's mother Greta is this in Monster Allergy. It's less that she stumbled across his secret at any point, and more that his ability to see and talk to supernatural beings is actually hereditary. She feigned ignorance and never pressed him too hard about any of the odd occurrences around the house. At least until halfway through the first season, when she learns that he used his powers to get into a situation that could have easily killed him, though they don't have an actual talk about her reasoning for another two episodes.
Zick: You can see [the ghosts]!? Greta: Of course, I can see them! They're my parents!
Moon Girl and Devil Dinosaur (2023): It's implied at the end of the first episode that Mimi instantly figured out Lunella was Moon Girl, and throughout the first season she subtly helps her granddaughter's superhero career. The season one finale episodes reveal Mimi knew from the beginning because she was one of the two scientists who built the portal Devil came from and was the original "Moon Girl" that Lunella named her superhero alter ego after.
My Adventures with Superman: In the fifth episode, "My Adventures with Mad Science", Jimmy cuts off Clark's long and awkward build-up to revealing his secret identity by telling him that he already knows his best friend is Superman. It turns out he knew about Clark's abilities since the first day they met in college, when Clark tried to pass offripping a door handle in halfas being a result of loose screws. As such, when Superman showed up, Jimmy immediately knew it was his roommate. He just never said anything over the years because he figured it was a sensitive topic, and was willing to wait for Clark to explain things. However, he is offended that Clark seemingly told Lois, the coworker they've both known for only a few weeks, before him.
It's heavily implied that Willow has already realized that Amity has a crush on Luz by the end of "Wing it Like Witches".
It's implied over the course of "Thanks to Them" (and confirmed in "For the Future") that Gus is aware that Hunter is a Grimwalker as a result of digging into Belos' memories in "King's Tide". He identifies with a character implied to be secretly aware that one of his crewmen is a clone, he specifically introduces the crewman in question as a clone apparently to give Hunter someone to relate to, and he doesn't react when Luz accidentally lets it slip.
In the Ready Jet Go! episode "Moon Circus", Carrot overhears from the kitchen that Jet is planning a surprise party for him. Carrot then has to keep the secret that he knows about the surprise party, but ends up telling Jet anyway.
It’s become increasingly obvious over the second season that Captain George Stacy knows that Peter is Spider-Man and is covering for both identities when necessary. A borderline case as Peter has by now been given more hints than he needed to figure that out for himself, but neither of them have gone so far as to say it outright.
It’s also implied, but never outright confirmed, that Curt and Martha Connors have figured it out too. Specifically, there is a scene in "Identity Crisis" where they’re both being interviewed by Ned Lee about the possibility that Peter might be Spider-Man, and at first, they laugh at the idea that Peter and Spidey might be the same person, but then they immediately get a "Eureka!" Moment where they seem to put the pieces together, and they realize that Peter being Spidey would actually explain a lot of unusual things about him. They then immediately end the interview by saying "no comment", implying that they figured out something big. However, we never find out for sure if they did figure it out or not, and if they have, they haven’t told anyone about it.
The writers were intending to reveal that MJ knew Peter was Spider-Man, but the show was cancelled before they had the chance to. There are still hints in the show proper, such as MJ being the only person that never gets annoyed by Peter's flakyness.
Star Wars: The Clone Wars: Anakin Skywalker and Padmé Amidala's Secret Relationship is the worst-kept secret in the galaxy. The only other people who are supposed to know are R2-D2, C-3PO, some of Padmé's handmaidens and guards, and implicitly Captain Rex. The people who are implied or outright stated to know, but aren't technically supposed to, include Obi-Wan Kenobi ("I hope you at least told Padmé I said hello."), Ahsoka Tano, Yoda, Bail Organa, and Palpatine.
Total Drama Pahkitew Island: After Sammy impersonates Amy to avoid elimination, she assumes only Jasmine knows about the Twin Switch. Turns out Chris figured them out as soon as it happened, but did nothing other than hint at it repeatedly to Sammy to make her squirm. Scarlett also knew, but assumed everyone else did as well and were just playing dumb.
Transformers: Prime: According to the tie-in book, Transformers: The Covenant of Primus, Alpha Trion was aware that Orion Pax was the reincarnation of "Thirteen", the last of the thirteen original Primes, long before he regained his memories and retook his original name: Optimus Prime. That being said, after regaining his Past-Life Memories there is no indication that Optimus was aware that Alpha Trion knew who he was, though considering that in this continuity, Alpha Trion is also a member of the Thirteen (which is why he knew who Orion Pax was), it's entirely possible he suspected as much.
In TRON: Uprising, Able (the boss at Beck's garage) seems to be awfully tolerant of Beck's frequent absences and strange explanations for those absences, as well as quick to scold Zed when he expresses frustration with "The Renegade's" antics. In "Grounded", he finally lets Beck know he knows: "What I have to say, I hoped I'd never have to say. So here goes. How did you become the Renegade?"
Peter is shocked to learn his Aunt May already knows he's Spider-Man.
During the events of the first Spider-Verse arc, Norman Osborn aka the Goblin finds out Peter's identity, but after he's brought back to his human form, it's revealed he's lost his entire memory of his time as the Goblin. Come the finale, though, Norman reveals his memory came back.
The Wacky Adventures of Ronald McDonald: In the final video "The Monster O'McDonaldland Loch", Birdie encounters the titular monster and is implored by him to keep his existence a secret. Near the end of the video, Ronald reveals to Birdie that he knew about her encounter with the monster when he asks her to get his help in combating a robotic version of the monster built by an evil inventor named Stiles.
Ronald: I know how to keep a secret, too.
In X-Men: Evolution, Amanda Sefton briefly sees Kurt with his image inducer turned off and using his teleporting powers once. This increases her interest in him, and she tries to pursue him romantically. Later, during an emergency where Kurt is reluctant to use his powers because Amanda would figure out the truth, she reveals she knows about him, and then just becomes a regular Secret-Keeper for the existence of the mutants until the Masquerade is broken.
Played with. Instead of a civilian keeping the superhero's secret, Robin knows Artemis' civilian identity (specifically, that she's from a family of supervillains) but doesn't let her know. He did almost bring it up when she was suspected of being The Mole, however. Also, since she doesn't know his identity, he Trolled her a bit when she transferred to his school.
Dick Grayson:[taking a selfie with her in their school uniforms] We'll laugh about this someday. [camera flash blinds Artemis; when she blinks, he's gone] Artemis: Who was that?
Superboy to Miss Martian. He knew she was a white Martian before they even became a couple, but he decided to let her tell him when she was ready.
During a Justice League meeting, Wonder Woman comments that nobody knew about Captain Marvel's real age, only for Batman to calmly announce that he did. Cap is visibly surprised by this. (Word of God says Batman knew everybody in the League's identity, even if they didn't volunteer the information.)
Dick is supposed to keep his identity a secret from his friends, at Batman's insistence, but shared the truth with his best friend, Wally; as a result, Wally knows that Batman is Bruce Wayne, and playfully teases the information in "Image".
