Two characters suddenly wind up in a relationship together, and decide for some reason to keep it a secret from everyone. The reason can be perfectly solid, e.g. one of them is the other's boss, but just as often it can be an ill-defined "I'm not ready for them to know" excuse. They remain awkwardly but successfully concealed for several episodes, speaking in Unusual Euphemisms, constantly leaving to Talk About That Thing and generating many a Fawlty Towers Plot — basically put, behaving in such a manner that requires all other characters to juggle the Idiot Ball like crazy.
Eventually they will be found out. This is not a variable — the Secret Relationship is made to be discovered. The only variation is when, how, and whether everyone finds out at once or just one or two people find out at first and have to help keep the secret until everyone else finds out. A common humorous scenario is that everyone knows, but don't care; or think it's funny watching them scramble to hide.
This can also be played for drama. Two people might be good friends, while aware that their parents, or the outside world, wouldn't approve of their friendship. In an attempt to prevent that from being discovered, the friends do everything they can to hide it, but sooner or later, hell will break loose. Romeo and Juliet may be the most well-known variation of this.
Naturally, a necessary precaution when Dating Catwoman.
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Meiko and Shinichi aka Nachan in Marmalade Boy, because he's her teacher. While Yuu finds out early on, the rest of the cast doesn't until they're caught and it becomes a scandal.
Later, Miki and Yuu get tangled up in one because they're stepsiblings and Miki's mother Rumi warned her not to fall in love with Yuu in the first place. She was actually joking, and once they tell the parents, they accept it. (It's handled differently in each media, though)
In Hanjuku Joshi, Yae and Chitose keep their relationship secret for a while, since Yae is afraid that their peers will judge them for being Schoolgirl Lesbians.
In School Days, Makoto and Sekai both decide to date (and sleep with) each other, while Makoto is still in a relationship with Kotonoha, which he also never really breaks off and continues to lead her on. It gets worse from there. Much, much worse.
Also invoked by others, like Haru and Rin, for the same reason: Akito is dangerously unstable and unlikely to ever accept them. When Akito finds out about Rin and Haru, she again flips out; she then goes confront Rin, Rin takes the blame on herself and Akito ends up tossing her from a second store window.
While most of their friends, and their parents, are well-aware of their relationship, Shuichi and Anna from Wandering Son have this type of relationship. It mainly has to do with the fact Anna is a model, and that Shuichi is Transgendered.
Ranma ½: Played for laughs when Ranma and Akane try to pretend they were secret lovers all along. Most people don't buy it though. Ukyo is convinced Akane is forcing Ranma to lie and the rest of the school knows the two of them aren't really Happily Married because they're not arguing.
Ohgi and Villetta of Code Geass have a relationship that remains hidden throughout most of the series.
In Naruto, Asuma and Kurenai had been seeing each other, although they tried to keep it quiet and denied that they were. The truth comes out with Kurenai's pregnancy, however, and all the other ninja suspected there was something going on between them anyway.
Mari and Akko in Girl Friends keep their relationship from their friends, probably because they're both girls and aren't sure how they would react. However, while Sugi-san had mostly figured it out even before Akko and Mari had (thanks to a rather transparent attempt at I Have This Friend by Akko), even in the epilogue set a year after they got together Tamamin still hasn't figured it out.
The Fullmetal Alchemist fan fiction Best Kept Secret uses this trope as its basic premise, exploring how the story might have gone if Roy and Riza were secretly married throughout the entire thing.
Many Soul Eater fanfics that pair Soul and Maka together have them trying to keep their relationship a secret. Usually it has more to do with Maka's Overprotective Dad than with their friends.
The "Sherlock" and "Harry Potter" crossover fanfic The Magic of Deduction has John and Sherlock fake breaking up to protect John from Moriarty. Slightly different as the two hardly had any contact with each other over the period of time in which they were "broken up"
This is the major driving force of Lawn Dogs. A 10-year-old girl and a widely distrusted 21-year-old lower-class man have a platonic friendship, that is tragically misinterpreted when discovered.
In Star Wars, Anakin marries Padme in secrecy due to the Jedi Code forbidding attachment.
In the film, Good Night And Good Luck, Joseph and Shirley Wershba have to keep their marriage secret from all their colleagues ( Pretty much all of them know anyway) as the rules at the time did not permit a married couple to work together. This is a case of Truth in Television as all the events of the film are factual.
Alien Cargo: As it’s against company regulation, Chris and Theta have to keep their relationship secret from their colleagues. They’re delighted that by chance they get to spend their shift out of cryosleep together, but later find out that this has exposed them to a dangerous virus that has infected the ship's living quarters.
Not to mention the fact that the medicine cats keep on falling in love even though they're not supposed to.
Matt and Kate in Starclimber. Kate's parents want her to marry someone else, and would definitely not approve of her marrying Matt because of his working-class origins.
Terence and Eileen in The Squire's Tales series. Terence is the main protagonist of the first two books; Eileen first appears in book 2, and they start a romance but don't make it public because Eileen is a noblewoman and her reputation would be ruined if she were known to be in love with a squire. The next few books focus on other characters, with Terence and Eileen making only cameo appearances. Then in the ninth book, it's revealed that they've been married since shortly after book 2, but have kept it a secret for fifteen years - though at least one other character can tell the moment she sees them together, and is confused when she finds out they don't share a room. Then at the end of the book, they decide "the hell with it" and have a second wedding in public... and Terence gets knighted, making it a non-issue anyway.
The People's Republic of Haven assigned political watchdogs to scrutinize the captains and admirals of every starship. In one instance, though, the watchdog and the admiral end up getting into bed with each other. "Conflict of interest" doesn't begin to describe it.
In addition, Honor and Hamish Alexander have a secret relationship for a while due to a number of circumstances, namely a) he's already married (though his wife, who's almost completely paralyzed, approves of and even encourages their relationship), b) Hamish is Honor's superior officer and, like virtually all militaries, fraternization between Manticoran officers in the same chain of command is forbidden, and c) Honor's adopted planet, Grayson, is very religious and does not approve of out-of-wedlock sexual relations (they're not on Grayson, but Honor's high status in Grayson society could have been damaged if it were known). The issue is eventually resolved when Honor marries Hamish and his first wife in a polygamous marriage (not that unusual in the Honorverse), taking care of the first and last issues, and by that point Hamish is the civilian head of the military, so the second issue is no longer a problem.
Christine and Raoul need to keep their relationship secret because Christine (rightly) fears what The Phantom of the Opera would do if he found out.
Monica and Chandler milked this for almost an entire season of Friends. And the other characters found out one... by... one.
Later, beautifully subverted in a plot where Ross is dating one of his students. They agree to keep it secret, as it's not something Ross would get fired over, but it is "frowned upon." Later, sick of keeping it secret, Ross announces the relationship to his fellow professors, who inform him he will be fired if the administration finds out (it was not just "frowned upon"). Thus, they go back into Secret Relationship mode.
Was well subverted in Northern Exposure. Joel and Maggie finally go to bed together, and after keeping it secret for about forty-five minutes they can't stand the subterfuge anymore and actually announce it to everyone in Roslyn's Cafe. Nobody cares.
Farscape - in the fourth season, Aeryn and John conceal their relationship and fake a break-up to prevent Aeryn and her unborn child being used against John by Scorpius.
The thing of it was, Aeryn herself was left in the dark for half a season. John had to conceal how he felt to make it look real and could only explain when an opportunity arose.
A less pleasant example is Chiana and Jothee behind D'Argo's back. The two begin an affair because of dissatisfaction with D'Argo's plans for the future (quiet married life on a farm). D'Argo finds out the next episode and is very, very unhappy.
In the British sitcom Executive Stress, a husband and wife must hide the fact that they are married from their employer. The employer has a policy that if two employees marry, one of them must quit or be fired.
Subverted in Battlestar Galactica (Reimagined) by President Laura Roslin and Admiral Bill Adama. Their close friendship (which has turned into a romantic and sexual relationship) is not really hidden at all, despite the conflict of interest that comes from the fact that they are the heads of the two branches of government in the Fleet (civilian and military). As of the back half of season four, they are living together and fairly affectionate in front of others.
Tyrol and Boomer, probably the first example in the series. He's a chief and she's an officer. Fraternization is frowned upon, so they have to keep their relationship a secret.
Billy and Dualla have some kind of a relationship that's not exactly public.
Dualla and Apollo have a somewhat secret relationship before they're married.
Apollo and Starbuck have a secret relationship after Apollo is married to Dualla and Starbuck is married to Anders.
Cally has an affair with HotDog. We only find out after we find out that Tyrol is a Cylon and he's not the father of the baby he thought was his.
Baltar's relationship with Number Six prior to New Caprica is a secret.
The secret lesbian relationship involving Admiral Cain.
Hardly secret. Cain kisses Gina in front of her officers.
The relationship between Kat and her former drug dealer.
In Scrubs, Dr.Cox and Kelso have entered into a secret friendship, which has tones of this. Kelso even describes it as "all the thrill of an affair, but without all that exhausting sex." When J.D. finds out, he's furious.
And earlier in the series, J.D. and Elliot think their relationship is this. It isn't.
Dr. Cox: "And, if you listen closely, you'll hear the sound of no-one caring."
David and Michelle on Kings: Michelle has taken a vow to devote her life to God, and in any case, her father is the King and probably wouldn't approve. (Though he may suspect...)
In Teen Wolf, Scott and Allison tried this, using Stiles as their liaison. It didn't work.
In the US version of The Office, there was Dwight and Angela's relationship from the second to fourth seasons (and then becoming a full-out secret affair when Angela is engaged to Andy in Season 5). Only Jim and Pam each find out individually, and the entire office learns just before both Dwight and Angela truly break up in Season 5's "The Duel".
The thing is, before Angela is dating Andy, Dwight and Angela keep it secret for no apparent reason; office relationships are not forbidden. They're just weird like that.
For the first four episodes after the Season 6 hiatus, Andy and Erin keep their newfound relationship a secret. Until they admit their relationship to everyone by the end of the episode.
However, they broke up in the next episode after Erin found out about Andy's history with Angela.
Blair and Chuck for a few episodes in Gossip Girl's' first season.
In a nod to the Star Wars reference above, when Jake and Miley were secretly dating in Hannah Montana they used the code names Anakin and Queen Amidala.
Sonny and Chad attempt this during the two-part episode that has them start dating. It works out about as well as one would think, and the So Random cast finds out (twice... it's hard to explain) before the second part ends. (And there was plenty of bad lying to cover up the first reveal.)
As of Season 3 of Castle Esposito and Lanie have begun a relationship that they're trying to keep secret due to working together. This is failing epically, as Esposito's partner, Ryan, Castle, and Beckett have clued in.
As of Season 5, Castle and Beckett are doing the same thing. As of the fourth episode of the season, Lanie has figured out that Beckett is dating someone but is maturely letting her have her privacy about who, Esposito is trying to figure it out, and Ryan already has.
Jimmy Palmer and Michelle Lee on NCIS, though it later turned out to be an Open Secret amongst Team Gibbs.
On an episode of The Wonder Years, Kevin eventually finds his Adorkable dance partner MargaretFarquhar to be genuinely sweet and interesting—but on a completely different rung on the junior high social ladder—so he suggests this trope to her as a way to balance it out. She takes offense.
Jeff in Community has had a couple. First season he had a brief one with Slater before they were outed by Pierce and then in season two it turns out he had 'friends with benefits' status with Britta for most of the year.
Played straight between Abby and Brody in Against the Wall. Eventually revealed in-universe and Richie, both Abby's brother and Brody's cop partner, is not happy.
Pretty Little Liars is chock full of this trope. This trope applies to practically every couple in the series, Ezria being one of the more dramatic examples.
Not to mention Spoby, Haleb, and Emaya at certain points.
Leslie and Ben in ''Parks and Recreation" had one of these in season 3, since Chris did not allow coworkers to date. Only Ann was privy to it, but Ron eventually found out and warned them that they were terrible secret keepers and everyone was going to find out eventually. They finally, reluctantly broke up when Leslie was given a chance to run for city counsel, knowing the scandal could destroy their careers.
The entire relationhip of Quinn and Logan on Zoey101, since both were embarrased to be dating each other. They were quite succesfull in keeping it a secret, actually their big reveal at the Prom, when they came clean about their romance, did come as a shock to everyone present at the moment.
When Doug and Carol reconcile on ER, they initially try to keep it a secret, due in part to Carol's hesitancy to fully commit(given Doug's previous track record for playing around, quite understandable). At the Christmas episode, she is confident enough in their relationship that she and Doug announce that they got back together at the staff Christmas party. Turns out most of the staff knew and had a running pool going as to when they would admit it!
Barney and Robin in How I Met Your Mother go the entire summer without their friends knowing about their Friends with Benefits arrangement (Future!Ted admits in a later episode that the other three were really, really passing around the Idiot Ball that summer). She says it's because they didn't want Lily forcing them to have The Talk, but he admits the lie just turned them on.
Arthur and Gwen in Merlin until the end of season 3 when they start making out in front of the castle.
Curly and Laurey in Oklahoma!. Inevitably, their duet "People Will Say We're In Love" is reprised as "Let People Say We're In Love."
Jason and Peter in bare: a pop opera have one of these.
In Street Scene, Mrs. Maurrant goes to lengths to conceal her affair with Sankey from others. Unfortunately, most of her neighbors already know about it.
In the execrable Full Motion Video game Phantasmagoria 2, the protagonist Curtis insists on this with his co-worker girlfriend. Which paves the way for freaky BDSM sex with the only other female co-worker.
One option for Damien's path in Magical Diary, at the end. For the best ending, you have to keep it a secret. Potsdam knows, no matter what, but she doesn't do anything besides suggest that you cover up your hickey. Failure to do so leads to your friends turning on you if they find out - but by this point, they've seen their worst nightmares about your relationship with him come true, so they're justified in believing that you're suicidal and possibly insane for trying to continue any kind of relationship with him.
In Mass Effect 3, DianaAllers' romance is this, as she says her career would be jeopardized if her relationship with a source came to light.
The Dating Catwoman variation is used in Evil Inc.., where Captain Heroic and Miss Match are married despite being a hero and a villain. Only their son, their parents and one of his allies knows. Additionally, each set of parents has never met the other set due to the risk of conflicts.
Winsbury and Janet in Gunnerkrigg Court, at least, until The Reveal is made in Chapter 34. In-comic, it's not clear exactly why its a secret; perhaps the fact that Janet is the Headmaster's daughter has something to do with it. Out-of-comic, it's a reference to the folk song "Willie O'Winsbury" (Child Ballad #100). The Willie and Janet from the song keep it a secret because Janet's dad is the King. Word Of God stated that the couple is hiding the fact that they're also "romantic dorks" which they also reveal in the strips immediately following the initial reveal.
Bruno and Corrie in Kevin & Kell; in the early years, Corrie rode on Bruno's back disguised as a sheepskin.
In the web series Shadow Of The Templar, both Simon and Jeremy keep their relationship a secret from everybody else. That's probably a good thing, because one is an FBI agent and one is a high profile Gentleman Thief. Thoroughly subverted in High Fidelity when Simon admits to his team and to his boss the nature of his relationship with Jeremy.
Principal Skinner and Edna Krabappel on The Simpsons: they keep it a secret for half an episode, get found out, get fired, hold the empty school hostage, then pretend to break up. Afterwards, they (literally) put their relationship back in the closet, with varied degrees of secrecy after that. It's one of the few Simpsons plots not completely affected by Negative Continuity.
Edna and Ned Flanders tried to keep their relationship a secret too. Or at the least, until Edna unintentionally revealed that she and Ned eloped some time ago.
Shaggy and Velma in Scooby-Doo: Mystery Incorporated. At first it seems like Shaggy's just afraid of commitment and using Scooby as an excuse, but his reasons for keeping the relationship a secret become more understandable once we see Scooby's hostile reaction to having Shaggy ditch him to take Velma to the prom.
Kick Buttowski gives us Kendall and Ronaldo, after Kick finds out about them in "Frame Story"... albeit, even the viewers are confused about wether they're together or not, consistently. Since that episode there have been numerous episodes in the second season where they're still dating, yet Kendall either breaks-up with Ronaldo, prefers Kick and even cheats on him behind his back (literally behind his back).
Young Justice Season 2 reveals that Red Arrow and Cheshire developed one during the Time Skip, including a (probably) secret marriage and a kid.
Romeo and Juliet could have learned a few valuable lessons from Ferdinand of Aragon and Isabella of Castille, who determined to unite both themselves in marriage and their kingdoms into the unified Spain. This they accomplished in defiance of both their families and the Church's ban on marriage between second cousins (which is what they were) besides through numerous secret letters sent to each other, a couple of clever ruses, Ferdinand disguising himself as a traveling merchant at one point, and a Papal Bull of dubious authenticity. In addition to their success in consummating their secret relationship, they also proved to be very cunning political partners. Seriously, their history sounds a lot like what Romeo and Juliet's tale might have been like if Niccolo Machiavelli had written it instead of Shakespeare. Today, every Royal House in Europe is descended from them - usually many times over.
Australian astronomer Ruby Payne-Scott was forced to marry in secret because the law did not permit married women to hold a permanent position in the Commonwealth public service. She was eventually discovered and forced to leave her position, despite being a pioneer in the development of radiophysics and radio astronomy.