Farnese in Berserk is kind of presented like this at first: girl on a holy mission who fights (sometimes). Thing is, she's actually revealed to have no combat skill whatsoever (women being at the head of the order for symbolic purposes), the voices she hears actually come from demons (Joan of Arc's enemies accused her of this), and she's a pyromaniac. She eventually becomes an actual witch.
In the wider Digimon canon, Darcmon is an angelmon specifically based on Jeanne. Her appearance in the film Digimon Frontier: Revival of the Ancient Digimon, however, is a subversion: Darcmon is one of the disguises used by the villain, Murmukusmon.
Code Geass: Nightmare of Nunnally puts a bit of Mind Screw on this. Initially C.C. is portrayed as being the actual Jeanne D'Arc, but later we find out that the real Jeanne cut a Geass emblem into C.C. and positioned her as a witch, then C.C. aided Britannia in capturing Jeanne, who at her burning cursed C.C., who was also burned as a witch.
Esther Blanchett of Trinity Blood was something like this in the light novels. She was the young orphan-novice who acted as the brave cross-dressing leader of the partisans in István and later on was hailed as Lady Saint. However, she turns out to be really the long lost heir of Albion and becomes Queen, subverting this.
Joan of Arc herself shows up in Axis Powers Hetalia... for about five seconds. Plus she's only listed as 'that girl', though it's obvious who the girl is. Fandom, however, has taken the concept of France/Jeanne and run wild with it. In volume four of the published manga (and the fifth anime season), France meets a young girl named Lisa, who might be a reincarnated Jeanne.
Joan of Arc is, well, Joan of Arc's clone in the series Afterschool Charisma. It's questionable whether she has visions or not since she does spend a lot of time staring into a mirror. She plans on pseudo-sacrificing herself (mimicking being burned at the stake, of course) in order to break the chains of destiny and hopefully live past her original's age of nineteen.
Sephiria Arks, the Lady of War from Black Cat. She leads a special military unit of assassins, is ridiculously skilled at using a sword, and her last name is probably a homage to Joan d'Arc.
Lyrical Nanoha has the last Sankt Kaiser, Olivie Sägebrecht. She was a young girl who found herself thrust into the position of leadership during a time of war before eventually dying for her goal to end the fighting, leading to others following her cause and ensure that her sacrifice was not in vain. In her case, her legend shot past sainthood and went straight to godhood as she's currently worshiped as the Christ-like figure of the Saint Church, the most prominent religion in The Multiverse.
The Authority: Every century has its Jenny, representing the driving force of society at the time. One of them Jenny Crusade in a musketeer outfit.
Film - Animated
Mulan has a lot of the elements, despite being based on a Chinese legend a thousand years older. Maybe Joan of Arc isn't so much the Trope Maker as the Trope Codifier.
Film - Live Action
In the extra features on Hard Candy, when asked which historical figure her character was most like Ellen Page responded "Joan of Arc."
Princess Leia of Star Wars might almost qualify except her down to Earth and snarky personality makes it an uneasy fit.
Sarah Connor from the Terminator franchise has aspects of this.
In Snow White & the Huntsman, Snow White is given the Joan of Arc treatment in many ways. She acts as a symbol of resistance to a foreign usurper, fights in plate armour, and is considered something of a living saint.
When asked to describe Katniss Everdeen of The Hunger Games, actress Jennifer Lawrence replied, "She's a futuristic Joan of Arc." Her co-star Donald Sutherland also compared Katniss to Joan. What clinches her role as Jeanne D'Archetype, however, is probably the whole "Girl on Fire" image which Katniss is given.
Rita Vratski from Edge of Tomorrow. The setting is even in France to push the connection further.
D'joan/Joan in the Cordwainer Smith story "The Dead Lady of Clown Town," although she's more of a nonviolent revolutionary with religious overtones than a warrior.
Ursula from the Slaves to Darkness trilogy managed to lead the fractured armies of the Empire to face the Chaos Warriors of the Norse in their own homeland. This led to an retaliatory invasion that nearly destroyed Kislev, but hey... What is interesting about her is that her possession of the legendary blade Ulfshard, the weapon of one of Sigmar Unberogen's own contemporaries, actually gave her a claim to the contested throne of the Sigmarite Empire in a time where every Elector Count was at the other's throat for the position. Various Counts attempted to leverage her in their own ways to gain power, which is ultimately the reason why her crusade against the Norse even happened. She spent her last days anonymously in a small convent, too. So consider her a Deconstruction.
Saint Sabbat in the Gaunt's Ghosts novel Sabbat Martyr has an origin story that is quite Joan of Arc-like (young farm girl with divine visions becomes a charismatic military leader and is eventually martyred.)
"Wazzer" in Monstrous Regiment: dresses like a man like everyone else in the regiment and receives visions from the spirit of the Duchess, a kind of spiritual protector/Virgin Mary figure for their country. But she also Deconstructs the trope, as she is not very good in a fight — unless you insult the Duchess — and seriously creeps out most of the other members of her regiment. Polly theorizes that Wazzer's abusive past caused her, somewhere along the line, to just snap.
Mina of the Dragonlance War of Souls trilogy is a subversion — she's very much the traditional image of Joan (teenage girl who is nonethless a deadly warrior and an incredibly inspiring leader on a mission from God), except that the voice she hears is actually that of the setting's traditional Big Bad. Mina, however, has no real idea that she's evil's tool and believes she's this trope played straight.
Laurana in the original Chronicles trilogy fits the trope very well. She never intended to be a leader, but after being incomparably badass at the High Clerist's Tower she found herself in command of the Knights of Solamnia and the armies of Palanthas.
In the Belgariad, Princess CeNedra takes up the role of figurehead for the army of her husband while he's off fulfilling prophecies and such, mostly to make a lot of noise and distract the bad guys. She may not actually BE the Jeanne d'Archétype, but she presents herself as this to her army, and plays the role to the hilt. She even goes so far as to have gold armor made (too thin to actually be protective, so she can actually move with it on) which... exaggerates her pettanko frame, to the gripes of the armorsmith tasked with making it.
Ash, in Mary Gentle's Ash A Secret History, is very much this archetype in some ways, as a female military leader in the fifteenth century who hears voices. Unlike her in other ways; she's not very religious, for instance.
After she kills the Lord Ruler, the people start to view Vin of Mistborn as something akin to this. Vin, who thinks of herself as little more than a magic-using assassin, is more than a little disturbed by the whole thing.
Holding the Zero, a novel by Gerald Seymour set in a Kurdish revolution against Saddam Hussein led by a teenage girl. She's shown to inspire several protagonists, but her entire revolution is a result of Kurdish and Western power politics — when the CIA and SIS pull out of the operation, most of her army runs for the hills except for a handful of loyal supporters, and she ends up being shot by the main protagonist (a British marksman) as she's about to be hanged by the Iraquis.
Katniss Everdeen from the The Hunger Games is a deconstruction. She's an Action Girl from humble origins who stands up to oppression to protect a loved one and becomes a beacon of hope for the rebellion. However, off camera she's actually a pragmatic survivor who never really cared about the rebel cause and is in it solely to protect her family. Later on when she starts having visions it's a result of trauma, drug addiction, and possible brain damage rather than any divine inspiration.
Live Action TV
Joan of Arcadia is an odd case, since it clearly references Joan of Arc but avoids many of the usual elements, apart from having a young girl carrying out missions from God as the protagonist.
Wonderfalls was loosely based on Joan, with Jay being urged to help people by strange voices — in her case, from inanimate models/pictures of animals.
Ambassador Delenn in Babylon 5 is an obvious example, being a mystically inclined woman who uses her charisma to lead in battle against a great enemy and inspires devotion and heroism in her followers. However she is a high class woman rather then a peasant girl.
Joan of Montreal, a one woman comedy special featuring Brigitte Gall, tells the story of a young French-Canadian woman chosen by God to defeat the English by being goalie for the Montreal Canadians in the last game of the Stanley Cup Final.
The sci-fi miniatures wargame Infinity takes this a step further, in that it has Jeanne d'Arc herself as a character that can be fielded. In reality, it isn't the actual Jeanne d'Arc (the actual warrior, for example, wasn't wearing Powered Armor) but is a "recreation" of her designed by the super-AI AELPH to serve as a battlefield commander for the armies of PanOceania, along with countless other Historical Domain Characters.
Some historical minis wargames do allow you to field the actual Jeanne (or at least a tin figure representing her)
Jeanne d'Arc is an actual NPC in Continuum, where she is a powerful time traveler who serves as a one-woman security force by calling in herself from other points in the timeline. Even more bad-ass, she knows her fate is to be martyred in France, and accepts it blithely, ready to head back when the time comes. It Makes Sense in Context, as the PCs themselves are also time-travelers.
"You Can't Keep a Good Girl Down" from Sally has a refrain beginning "I wish I could be like Joan of Arc."
Leliana of Dragon Age: Origins has shades of this character, having a French accent and claiming to hear the voice of The Maker, but the more obvious example is Andraste, who culturally takes the role of Jesus, but whose actual story reads as more a cross between Joan of Arc and Boudica.
Obviously the story of Jeanne D Arc is based very closely on the actual story of Joan of Arc, but with many additions and imaginings (like a magic gauntlet that transformed her into a valkyrie, for example).
Likewise, La Pucelle is another game with a Joan-like heroine, and is also named after one of her titles (French for "The Maiden"). Though Prier is a little more selfish than most archetypes, and her story may take a horrendously wrong direction. If you allow the dark energy on a stage to build up, a portal into the Dark World eventually forms. If Prier kills a significant number of demon lords and overlords while in the Dark World, she eventually gathers so much demonic energy that she becomes an overlord herself. (Interestingly enough, this event does not end the game, which also makes Prier the first canon example of a non-evil Demon Overlord, as well.)
Monica of Yggdra Union. Yggdra herself, as her title is La Pucelle.
In a way, The Boss from Metal Gear Solid 3, although she's older than the usual examples. However, during World War II she became a military leader at an early age, she fought for her country, and once the truth about her fake defection comes out, she can be seen as a martyr.
Micaiah in Fire Emblem: Radiant Dawn. She is named the Silver-Haired Maiden, she leads La Résistance, she's the one to find the lost heir to the throne, and everyone, enemies included, agrees that she's the one the people of her country will follow to the death, rather than the king. And Micaiah becomes the Queen of Daein in the end... though if she wanted to, she could've claimed her right to the Empire of Beignon instead. (Her little sister Sanaki remains Empress, however.)
In the MMORPG Atlantica Online, one can hire a Lady Knight mercenary, whose final upgrade is Jeanne d'Arc (or Joan of Arc). She is a sword type and is an extremely good tank.
The Witcher 2's Saskia the Dragon Slayer fits this trope to a tee at first glance, a peasant girl who had by all accounts slain a dragon and is much beloved by the common folk who leads a peasant uprising, and helps to defend the city of Vergen from an invading army. She dreams of creating a queendom where humans, elves and dwarves live together as equals. An uncommonly noble goal in the Crapsack World of the Witcherverse (whether she is successful or not varies depending on your game choices). But there is a twist... She is not actually a dragonslayer, she is an actual dragon, able to assume human form. The whole Dragonslayer story was cooked up by an elvish rebel named Iorveth, to help endear her to the people. Why she feels the need to fight for the common folk is a bit unclear, but perhaps she just felt the humans were doing it wrong and decided to show them how do to it right.
Jeyne Kassynder of Dungeon Siege III, who in the backstory riled up the populace against the 10th Legion in order to avenge the slain King, her father, and exterminated them. However she's actually the Big Bad of the game since the main characters are attempting to rebuild the Legion.
The "Sword Magess" from Wild ARMs 2 was obviously based on Joan, from being chosen by a divine being (a wolf) to save her world, to having her humble family become nobility after her death.
Emilia Nighthaven from Heroes of Might and Magic IV, who goes from a glassblower's child to the Queen of Great Arcan during the course of the Order campaign.
Byakuren Hijiri from Touhou. A religious figure, is/was persecutednote being an immortal she can't be a martyr, has a fanatical cult following, and is thrust into a conflict greater than herself. She's not exactly "holy", though.
Should be mentioned Byakuren was inspired by Japanese religious concepts and old legends, and is actually based on a Historical-Domain Character herself.
Sophitia from Soul Calibur is given a mission from her god, Hephaestus, to destroy Soul Edge (she only half-succeeds). In the Dreamcast game, her third costume is in heavy armor, greatly resembling most depictions of Joan.
Hilde, who debuts in the fourth game, fits the description even more; in fact, she seems to have been specifically designed for this role. (If anything, she's the only female in the game who is always fully armored and thus avoids the Stripperific Trope that the others do, unless a player undresses her in Character Creation mode.)
The Sons of Abraham expansion of Crusader Kings II has an event chain where a lowborn woman with an insanly high martial stat offers her services. She can serve as marshall (normally a male only position), and several other events delve into her hearing the voice of Jesus.
World of Warcraft: Warlords of Draenor introduces a draenei named Yrel, who starts as a naïve priestess but steps up to become a heroic paladin when the Iron Horde begins to attack her people.
An older example can be found in High General Brigitte Abbendis, leader of the Scarlet Onslaught in Wrath of the Lich King. Abbendis had many of the Joan of Arc features such as being a warrior lady, leader of a crusade and fervently religious; in the Death Knight starter quests we see documents that describe her as being struck by holy visions and hearing voices. Unfortunately, the 'holy' visions and voices are actually sent by a demon, and the Scarlet Onslaught is composed of genocidal zealots.
Saber from Fate/stay night is actually a very straight example. She is an expert swordswoman, was born humble but became the leader of her people, pretended to be male, and even eventually died because she was betrayed by her people. It's often the first guess as to her true identity. Of course, that's assuming she's based on a female hero...which she's not. She is in fact a Gender Flipped King Arthur, Arturia Pendragon. In Fate/Zero she actually is mistaken for Jeanne d'Arc by a character who was Jeanne's contemporary: the Caster of that Holy Grail War, who once was Jeanne's companion Gilles de Rais.
Fate/Apocrypha features the actual Jeanne d'Arc, who obviously also plays this trope straight.
In life, Jeanne of Gunnerkrigg Court, a French Lady of War, and human sacrifice in the early days of the court. Now she's a ghost stranded on the shore of the river who is "beyond even the Guide's reach."
Subverted and possibly deconstructed with Jone (sic) Half-Orc in Yet Another Fantasy Gamer Comic. Jone starts as a sympathetic young character with humble origins who just turns out to be a natural fighter and on a mission from the orc-god Gruumsh; it's too bad that her eventual army of followers consists of self-deluded fanatics (including a self-styled prophetess "interpreting" Jone's wishes as she sees fit, since their savior-figure is unfortunately mute) and that Jone herself gets so caught up in her "crusade" that she ultimately ends up going Ax-Crazy beyond redemption.
In Times Like This, Joan is rescued from her execution by Cassie and Matt (with a little help from a Decoy Getaway). She now lives in the present time as Joan Arquette. The storyline begins here.
Pucelle of the Whateley Universe. She's really a deconstruction, because she sees herself as a Joan of Arc figure and pushes toward that image, while irritating the heck out of her dormmates and classmates.
Comically subverted on Clone High, where the Joan of Arc clone is an angsty goth chick. In one episode, she thinks she hears the voice of God telling her to spread His word, but it's actually a radio station she's picking up through her braces.