The Marvel vs. Capcom series has featured a number of secret characters that can only be chosen by fulfilling specific conditions or imputing a code in the select screen. This included unique characters (such as Akuma and Roll) as well as simpler palette swaps of standard character with some unique gimmick or theme (such as Gold War Machine and Shadow Lady). By fulfilling certain requirements during Arcade Mode (such as not losing any round or winning with a specific number of Hyper Combo finishes), the player can also face these secret characters before the final boss.
Boss characters are often also unplayable in the original Arcade release and become secret playable characters in the later console ports.
- Akuma: The very first secret character, and often called the origin for the entire crossover series. Featured with his appearance from Super Street Fighter II Turbo, Akuma is a secret unlockable character (and boss) in all versions of the game.
- Juggernaut: The unplayable mid-boss in the original release, Juggernaut can be unlocked in the PlayStation and Saturn ports. He's only usable in Vs. Mode, however.
- Magneto: The unplayable final boss in the original release, Magneto becomes a secret unlockable character exclusive to the PlayStation port. Like Juggernaut, he's only usable in Vs. Mode.
- Doctor Doom: The game's mid-boss character, he's actually unlockable in the Arcade version, but it requires the Arcade to be set to "Free Play", which can only be done by the owner of the machine. He's a secret character in console ports, selectable after beating the game once.
- Thanos: The game's final boss, he's unlockable in a similar manner as Dr. Doom in the Arcade version, also requiring the Arcade to be set to "Free Play". He's unlocked in the console ports after beating the game once.
- Anita: Anita is a unique (and unfinished) secret character only unlockable in the Japanese version of the game (she exists in the English version, but can only be used through hacking). She requires a similar trick using "Free Play" in the Arcade version, and a code sequence in the console ports. She later became a legitimate (but still unfinished) secret character in Marvel vs. Capcom Origins.
- Akuma: "Technically" a secret character, Akuma is simply outside the character select screen, and pressing up while on the top row will display him.
- Apocalypse: The gigantic final boss, Apocalypse is only selectable in the PlayStation port of the game, although only available in Vs. Mode.
- U.S. Agent: A palette swap of Captain America (in spite of being a distinctly different character in the Marvel universe). Outside unique victory quotes, he plays exactly the same as the original.
- Mephisto: A palette swap of Blackheart, his son. His physical basic attacks ignite the opponent when they connect, but this is just an aesthetic difference.
- Armored Spider-Man: A gray version of Spider-Man with limited super armor and slightly lower jumps. He's based on a metallic suit Spider-Man wore in the comics.
- Mecha-Zangief: A version of Zangief with Hyper Armor, meaning he can't be stunned out of his moves, but in return can't block and jumps really low. He also gains two new moves. He became a transformation Hyper for Zangief in the sequels. Often mistakingly called "Evil Zangief".
- Dark Sakura: A sunburned version Sakura who throws fireballs horizontally instead of diagonally, and also has Akuma's Ashura Senku and Shun Goku Satsu Hyper. Became a transformation Hyper for Sakura in Marvel vs. Capcom 2. Often mistakenly called "Evil Sakura".
- Shadow: A darkened version of Charlie with powerful super moves that have incredible start-up lag. Represents a version of Charlie experimented on by Shadaloo and M. Bison, and who now struggles to break free from its control and stop Bison.
- Apocalypse: Now the game's mid-boss, Apocalypse is again an exclusive secret character in the PlayStation port, where he now can be used in Arcade, Vs. and Training Mode.
- Cyber-Akuma: A cybernetic amped-up version of Akuma. Created by Apocalypse and also the final boss. Can be unlocked in the Saturn and PlayStation ports as a secret character.
- Roll: Although based on Mega Man gameplay-wise, Roll is a unique character with her own sprites, victory quotes and ending.
- Lilith-Mode Morrigan: A form of Morrigan with Lilith's palette and moves.
- Shadow Lady: A dark palette swap of Chun-Li with different, cyborg-themed moves. She represents a Chun-li brainwashed and cyborgized by Shadaloo in an identical manner to Shadow.
- Hyper Venom: An orange palette swap of Venom, popularly called "Red Venom" by fans despite being obviously orange. Hyper Venom is the fastest character in the series, with all his moves having an afterimage effect, but in return, he takes about two times more damage than everyone else. He also has a few different moves as well.
- Gold War Machine: A golden palette swap of War Machine, popularly called "Gold War Machine" by fans. Mega War Machine has Hyper Armor, which means he cannot be hit-stunned or dizzied, but in return can't block, moves very slow and can't jump high. All his laser attacks are replaced by missiles as well, and he loses the "Repulsor Blast" special.
- Orange Hulk: An orange palette swap of Hulk. This version of Hulk gains speed at the cost of his Super Armor and his movelist is taken from his previous appearance in Marvel Super Heroes.
- Onslaught: The game's final boss, he becomes unlockable in the PlayStation port (selectable in all modes) and the Dreamcast port (in an exclusive mode called "Onslaught").
- Shadow & Sentinel: These two are secret Special Partners. Unlike the other assists (who are randomly selected every match), they can only be selected by holding specific button combinations.
Marvel vs. Capcom 2/3
Marvel vs. Capcom 2: New Age of Heroes and Marvel vs. Capcom 3: Fate of Two Worlds don't feature any secret characters per see, instead having a number of unlockable characters (who are otherwise standard) that must be obtained by specific means:
- The Arcade version of Marvel vs. Capcom 2 unlock characters as time goes on or after winning single player several times.
- Console versions of Marvel vs. Capcom 2 require characters to be bought with in-game points (gained by playing in any mode) in the "Secret Factor" shop.
- Marvel vs. Capcom 3 requires characters to be unlocked by accumulating in-game points, gained by playing in any mode.
- Galactus: The game's final boss becomes unlockable in the Ultimate version of the game, only usable in a special "Galactus Mode".
- The Marvel-side secret characters (as well as bosses and Cyber-Akuma) all have the same generic ending: they appear doing a stance in front of the Hyper Combo background while the words "Congratulations! You've beaten the game with a secret character!" appears underneath them.
- This doesn't apply to Dr. Doom and Thanos in Marvel Super Heroes (where they have unique endings) and Galactus in Ultimate (who has his own ending when the player loses against him and doesn't continue).
- The Capcom-side characters in Marvel Super Heroes vs. Street Fighter have the same generic ending in the English version, but unique endings in the Japanese original.