The Marvel vs. Capcom series has featured a number of secret characters.
- U.S. Agent: Although a distinctly different character than Captain America in the Marvel universe, he is just a palette swap in the game.
- Mephisto: A palette swap of Blackheart. His physical basic attacks ignite the opponent when they connect, but this is just an aesthetic difference. Blackheart is his son.
- Armored Spider-Man: A grey version of Spider-Man that has limited armor, based on a metallic suit he wore in the comics. He jumps sightly lower than before due to the heaviness of his armor.
- Mecha-Zangief: A version of Zangief that can neither block nor be put into hit stun. Because Zangief can turn into this character in later installments to the series, many mistakingly called it "Evil Zangief".
- Dark Sakura: A sunburned Sakura who throws fireballs horizontally instead of diagonally, and also has Akuma's Ashura Warp and can perform the Shun Goku Satsu (sometimes mistakenly called Evil Sakura for this reason).
- Shadow: A darkened version of Charlie with powerful super moves that have incredible start-up lag. A version of Charlie that suffered harsh experiments (brainwashed) at Shadaloo's hands, now serves them. By Marvel vs. Capcom though, he's broken free of their control.
- Cyber-Akuma: A cyborg, amped up version of Akuma created by Apocalypse. Also serves as the game's final boss. Called Mech-Gouki in Japan.
- Hyper Venom: A sped-up form of Venom with afterimages, called Red Venom by fans, despite being obviously orange. He's the fastest character in the VS. Series itself, but he takes about two times more damage than everyone else. This could be based on another Marvel Comics villain Carnage as he is faster and stronger than the original Venom.
- Mega War Machine: A form of War Machine that cannot block, but also cannot be hit-stunned or dizzied. Typically called Gold War Machine by fans. His power and defense increases dramatically, but his movement speed is greatly decreased.
- Lilith: A form of Morrigan with Lilith's palette and moves.
- Orange Hulk: A speedy version of Hulk with his moveset from Marvel Super Heroes sans Hulk's super-armor.
- Shadow Lady: A cyborg palette swap of Chun-Li, similar in style to Shadow from Marvel Super Heroes vs. Street Fighter but with a different variety of cyborg-based moves. Her speed also increases, similar to Shadow.