Because Long Hair Is Feminine, when a girl has short hair it tends to mean she's decidedly less feminine than the average girl, perhaps even a Tomboy or Action Girl. This choice of having short hair usually indicates a girl has a more masculine personality, is tough and aggressive, or is lacking in vanity, perhaps being business-like and brainy. Girls may cut their hair short because they don't want to put up with the maintenance that longer hair requires. Other times it's short so no one can easily grab it in a fight, which Braids of Action are sometimes prone to be.
The contrast of a short haired girl with a long haired one can sometimes be used to portray a Tomboy and Girly Girl. If taken to extremes, a girl with Boyish Short Hair could be a Butch Lesbian, many of whom have this as an indicator. May be the result of an Important Hair Cut, with the new short hair being an indicator that the girl is ready to take action. Also sometimes necessary for a girl to go undercover as a Sweet Polly Oliver.
When an Iron Lady or other woman in power wears short hair, it's usually not this but the much more carefully styled Power Hair, which says feminine but no-nonsense.
Compare Tomboyish Ponytail and Long-Haired Pretty Boy, the direct opposite of this trope. Contrast Long Hair Is Feminine. Also, compare it's ancestor, the '20s Bob Haircut, and possible successor, the Sci-Fi Bob Haircut. A subtrope of Expository Hairstyles.
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Anime and Manga
Kino in Kino's Journey has boyishly short hair. She is a Bokukko variant of Tomboy and often uses masculine pronouns to refer to herself.
Tatsuki has short, dark spiky hair and is the class tomboy. She's a karate expert who trained Orihime to black-belt level. Chizuru once comments that she would have found Tatsuki attractive if not for the masculine vibe Tatsuki always gives off. After the time-skip, she grows out her hair.
Soifon has short hair with two tightly bound braids. She is the Gotei 13's top ninja and neither gives quarter nor asks for it. She's a grim, aggressive personality who has worked hard to build a ruthless reputation. After the time-skip, she loses the braids and her hair becomes shorter than ever.
Rukia is a short-haired action girl. She's had a rough life, and possesses the rough, aggressive personality to match.
Jackie Tristan is X-Cution's only physical fighter, whose power centres around improving her kick-boxer attacks and morphs her clothing into a Badass Biker theme. Although appearing to be quiet and aloof, she becomes very rough and aggressive in battle.
Sapphire from Pokémon Special won't be winning any awards for femininity anytime soon and her hair isn't particularly long; the bangs are rather exagerrated though. Averted in the past where she was a big girly-girly and sported the same haircut.
Dirty Pair Flash: Kei makes up the tomboy half of the Lovely Angels. Though she and Yuri are among the 3WA's top trouble consultants, she's better known for her hair trigger temper and her itchy trigger finger. Which often spells disaster since she packs a friggin' hand canon! She's also a Lad-ette.
Mariya from Otome wa Boku ni Koishiteru: Every character, including the male lead, is The Ojou. Mariya is less ladylike than the rest of the cast, including the male lead, and she drops her facade only when she's alone with him. While still feminine (a true tomboy would be very out of place at a high-class all-girls school) she occupies the tomboy role.
Code Geass: Kallen is a Ms. Fanservice version of this. She is the Black Knights Ace Pilot and Lelouch's bodyguard. Her short hair indicates that she is not to be trifled with.
Princess Nine: At least four, and possibly five or six, of the girls have Boyishly Short Hair. This is a show about girls playing baseball on even terms with boys so tomboys are to be expected.
Haruka Tenou/Sailor Uranus is a short-haired Bokukko, in explicit contrast to her lover, long-haired and feminine Michiru Kaiou/Sailor Neptune. She often wears masculine clothes in real life — not because she's specifically crossdressing, but just because she likes them. (Though it should be mentioned that this happens more in the anime than the manga).
Ami Mizuno/Sailor Mercury is also known for her short hair (although it's worn in a bit more feminine style) which is used to highlight her intelligence. When a possible future version of her was shown with long hair the fandom had a collective fit.
Toyed with in the case of Ukraine from Axis Powers Hetalia, who has extremely short hair and dresses like a boy, but is more of a Nice Girl in personality.
Played straighter with Belgium, who's quite straightforward and has wavy hair that reaches to her neck.
Allenby from Mobile Fighter G Gundam has very short blue hair and a boisterous, fun-loving and fight-loving attitude. Ironically, her Gundam has a very girly aesthetic with very long blond "hair," which actually serves as radiator fins for her Berserk Mode.
In Fushigi Yuugi, Yui did once have long hair, but cut it short in 8th grade to avoid all the attention she was getting from boys. She is noticeably more hot-tempered and considerably less ditzy than Miaka.
Tomboy Scout Finch has short hair in the film version of To Kill a Mockingbird (in the book, her hair length is not mentioned).
The main character in Train is shown to have cut her hair short in the end, after killing all the villains. It also probably symbolizes how she's serious about being on the wrestling team now, since witnessing your teammates being horribly tortured to death will apparently do that.
In Tomboy, Laure's haircut is sufficiently boyish that no one sees any reason to doubt her when she introduces herself as "Mikael".
Heroines Alanna and Keladry, both female knights, wear their hair short in the Tortall Universe books, being tomboys. Alanna went undercover as a Sweet Polly Oliver, but Keladry didn't, she just keeps it short because it's practical. Subverted by a later (but chronologically earlier) heroine, Beka, who despite being boyish and knowing that short hair is better in combat, keeps her long hair (as her one vanity), but braids a strip of spikes into it so anyone who grabs it in a fight will get a nasty surprise.
Most women above a certain age in A Brother's Price have short hair; the Whistlers in particular, whose grandmothers were soldiers, keep short military-cropped hair, and Eldest disapproves when Corelle starts growing hers out. In this world, it's the men who have long hair.
Vin in Mistborn starts out with this; it's quickly established that she wears her hair so short, and male clothing all the time, because she's very frightened of appearing feminine (and therefore, she thinks, weak) in front of other thieves and criminals. She grows it out a bit as she gets more comfortable with her femininity later in the series, but never so long that it would get in the way in a fight.
In the Dresden Files novels, we have 5' tall Lt. Karrin Murphy who wears her blonde hair short. She is the epitome of Badass Normal (is a master of firearms and a wide variety of martial arts) and works on an X-files style job of the Chicago police department. According to Harry, "she is so cute I want to put her in my pocket, but she'd break my arm if I ever said that." She and Harry have so much UST that several people in-universe have commented on it.
In the Dragonriders of Pern novels, we have some female dragonriders who keep their hair cut short. This is a practical choice, since they a) wear helmets and b) fly freaking dragons. Long hair would get in the way.
Gabrielle, Xena's sidekick on Xena: Warrior Princess provides the picture for this trope, and is also a perfect example, with her impromtu haircut being a symbolic conclusion to her Coming of Age Story, and of her maturing from being Xena's young sidekick and protegee, to a mature, independent, strong woman, and fighter, with skills on par with Xena's own.
Djaq from Robin Hood. The first series involved her as a Sweet Polly Oliver with cropped hair; by the second series she was no longer hiding her gender, but kept the short hairdo.
Captain/Major/Lieutenant Colonel/Colonel Samantha Carter of Stargate SG-1 is a good example. She's definitely brainy (an astrophysicist) and an Action Girl (she didn't get all those ranks for nothing.) However, she doesn't have much of a stereotypically masculine personality (though she is a Straw Feminist for the first couple of episodes) and she is definitely portrayed as super hot, though not sexualized. This is in large part justified by Air Force dress codes, and the show's military advisers were known to complain if Sam's actress Amanda Tapping let it get too long.
Starbuck, The Lad-ette and Ace Pilot from Battlestar Galactica (Reimagined). She tends to reject many staples of femininity (for example she has little to no interest in having kids) in favor of trying to outdo the boys: fighting better, being tougher, drinking more, sleeping around more, etc. Notably, the only time when she in a position of helplessness for a prolonged period of time, (being a Cylon prisoner on New Caprica during the entire occupation) is also the only time that her hair grows out.
Arya, the feisty tomboy from Game of Thrones. She loathes medieval female roles such as sewing, cooking, and dreaming of marrying a prince, and instead prefers beating her older brother at archery, learning how to fence, and so on. Cemented in season 2, when Tywin notes her unusual passion for history and warrior women from the past, and says that most girls prefer romantic tales about maidens with flowers in their hair and such. Arya's response? "Most girls are idiots."
Meg's original vessel had pretty short hair in Supernatural.
Actually, Meg's vessel originally had longer hair (up to shoulder length) and wore girlish clothes. When Meg possesses her, she cuts her hair and "dressed [her] like a slut". Her boyish short hair is a plot point to show how horrifying it is when demons possess and control humans.
Chie Satonaka from Persona 4 has shorter hair than her friend Yukiko, and is into more "boyish" things like martial arts. This trope is later taken to its logical conclusion when Naoto Shirogane is revealed to be a BifauxnenSweet Polly Oliver... with, naturally, boyishly short hair.
Bloody Roar: Primal Fury: Jane Gado, bka 'Shina'◊, is a highly trained mercenary and the adopted daughter of Alan Gado. She's known for her frankness and tenacity both on and off the field of combat. Her most striking feature is her spikey blonde hair, which resembles a lion's mane.
Soul Calibur II: Cassandra Alexandra◊, is another example. Unlike her sister, Sophitia, she's brash and somewhat impulsive, but usually means well. In the fourth game, she's determined to destroy Soul Edge and free her sister once and for all. The length and style of her hair varies depending on the costume the player selects, but it's usually kept short.
Kumatora from Mother 3 has this. Likewise, she hates wearing dresses and other girly clothes, often uses less-than-elegant language, and is overall depicted as a tomboy. Interestingly enough though, her Boyish Short Hair is pink.
Mass Effect: Female Shepard's hair can only go past about chin length with modding; most options range somewhere between "short ponytail" and "recently shaved". Also, of your female teammates in 2 - those that have visible hair, anyway (which discounts Samara, Tali and Kazumi) - the more conventionally feminine (although still badass) Miranda has long hair, while The Lad-ette Jack has a recently shaved head, and her Character Development into a more well-rounded and less Ax-Crazy persona is marked by letting her hair grow out a bit.
In The Order of the Stick Haley's hair is cut down to this style due to the petty cruelty of her spiteful rival, Crystal, who also sports such a cut. While Haley does become more action orientated around the same time, (she receives a major upgrade to her bow, making her even more The Archer than she was before, gets a wicked melee weapon rather than being helpless in close quarters combat, concludes her rivalry with Crystal, etc.) she's also rather uncomfortable with the look and buys a new, somewhat skimpier set of armor to show off that despite the haircut, yes, she is a girl. And while the cut lasts awhile, (about 140 strips) she also takes advantage of the first chance she finds to magically grow her hair back out.
Michelle Williams keeps it short In Memoriam of her late boyfriend, Heath Ledger, whom apparently liked her hair short like that.
Ginnifer Goodwin adopted this kind of hairstyle in more recent years, on the grounds that she's a self-proclaimed lazy person, and that managing her long hair was a hassle, between cowlicks, frizz, split ends, among other issues.