Hackette

"Trinity: My name is Trinity.

Neo: Trinity. The Trinity? That cracked the IRS d.base? Jesus.

Trinity: What?

Neo: I just thought um... you were a guy.

Trinity: Most guys do."

The Cops are hot on the trail of a hacker who is bringing down banks, shutting off traffic lights, and just generally causing mayhem.

They are given a list of possible suspects, all of whom happen to be men. After either narrowing down the list to one or two suspects, or dismissing all the suspects completely, the hero or his sidekick stumbles onto a startling revelation. The Hacker is a woman.

In the minds of all officers of the law and FBI agents (even female ones), hackers are exclusively male, and having a second X chromosome excludes you from any suspicion for anything having to do with computers or technology in general. When the truth is revealed, the notion that nobody previously thought a woman was capable of such things is either tossed aside, or even ignored altogether.

This trope only counts when everyone thinks it's a boy and it's later revealed the hacker is a female. It is not a list of generalized female hackers.

This is a sub-trope of Samus Is a Girl and happens to be the techie sister of the Wrench Wench.

Anime and Manga

 * Everyone in Cowboy Bebop thinks Radical Edward is a boy, even after meeting her. Imagine the shock when her father shows up and gives his "baby girl" a hug!
 * In Princess Lover, Teppei is surprised to learn that his maid, Yuu Fujikura, heads an entire team of hackers (all maids, like herself). It even becomes a pivotal plot point, late in the series, when she spearheads a cyberspace counter-offensensive to regain control of the Arima Building from a group of terrorists, while simultaneously helping to disarm several remote detonated charges planted throughout the building.
 * Gundam Wing has Hilde Schbeiker. While aboard White Fang's orbital base, Libra, she hacks into their mainframe to access and download vital information on Vayette and Mercurious: their latest and most advanced in their line of mobile dolls.
 * Nene Romanova fills this role in Bubblegum Crisis. Much like the Princess Lover example, it becomes a plot point when Nene uses her hardsuit to hack into the AD Police mainframe (unbeknownst to her fellow officers) to regain control of the building from a terrorist and his team of rogue boomers. While, at the same time, guiding the police chief's neice to safety via the intercom.

Film

 * Sandra from Cube 2: Hypercube.
 * Acid Burn from Hackers. She was an alpha hacker so she had a coterie of boyhackers who thought she was awesome, but Crash Override was surprised to discover she was a girl.

Literature

 * Lisbeth Salander from The Millennium Trilogy uses this to help her hide from the police.

Live Action Television

 * Claudia, when she is hacking into the Warehouse in the first few episodes of Warehouse 13, is spoken of with male pronouns until they learn her identity.
 * Penelope Garcia from Criminal Minds is happy to surprise supervisors and people from other precincts with the fact she's a female.
 * The Lone Gunmen has a female hacker whose real name was never revealed, but she went by Yves Adel Harlow most of the time. All her aliases were anagrams of Lee Harvey Oswald.
 * An episode of Burn Notice featured a girl hacker. Not only was the fact that she was an attractive teenage girl a surprise, but she also turned out to be utterly vicious and cold-blooded, as evidenced when she drugs Michael and then ties him to a chair and rubber-bands a plastic bag over his head in an attempt to kill him via asphyxiation (luckily, Michael manages to talk his way out of it).

Web Comics

 * Miho from Megatokyo caused a massive crash of the Endgames MMORPG servers and asks Piro if he was surprised to learn the aforementioned hacker was a girl.

Truth in Television

 * This is Truth in Television for most female programmers and computer technicians (whether they fit the general usage of "hacker" or not), since it's a very male dominated profession.
 * That said the Ur Example would be Ada Countess of Lovelace; who wrote a series of instructions that could have been executed by Charles Babbage's Analytical Engine (which would have been a Steampunk computer, were it built) and is often considered the world's first computer programmer (in the sense she wrote the world's first computer program).
 * The techs who maintained the world's first computer (Collosus) were mostly women from the Women's Royal Navy (or "Wrens").
 * Susan Thunder.
 * Kristina Svechinskaya, dubbed the "world's sexiest computer hacker".
 * The Chinese female hacker collective CN Girl Security Team.
 * Adeanna Cooke, who's also posed for Playboy.
 * Ying Cracker.
 * "Kayla", a suspected member of Lulz Sec in the HB Gary Federal leak, originally thought to be Laurelei Bailey.
 * There's a Not Always Right story about a guy calling tech support/bringing his computer back to the store and demanding to talk to a male employee, being incapable of accepting that women can know enough about computers to help with his problem.