In Battle City, Kaiba's Deck takes on several traits of a Virus Deck, which focuses on removing cards from his opponents' Decks and leaving them with limited options. One of the main strategies in this Deck includes using "Crush Card Virus" and "Virus Cannon" to mill his opponents' Decks, while also attempting to Summon "Obelisk the Tormentor" for the finishing blow. His "Obelisk the Tormentor" is supported with "Soul Exchange", and if that fails, he uses his "XYZ" monsters as offense until he is able to Summon "Obelisk".
The Virtual World Deck is very similar to Kaiba's Battle City Deck, though with more emphasis on Dragon-Type monsters, and without his Egyptian God (as the Virtual World's Deck construction list excludes the God Cards).
During the Waking the Dragons arc, Kaiba uses a Virus/Critias Deck. Kaiba's Deck evolves considerably, as he begins to include many more Dragons in his Deck, while also gaining "Fang of Critias", and still supporting "Blue-Eyes White Dragon" and "XYZ" monsters. He supports many of his Trap Cards with "Fang of Critias", creating powerful monsters to defeat the opponent.
Kaiba Duels once in this arc as well, against Yami Bakura, but the Duel is not finished because his opponent leaves in the middle of it. Against Bakura, he included cards from previous arcs, focusing mainly on his "Blue-Eyes White Dragon". Kaiba uses cards from previous arcs while he's in ancient Egypt to protect himself and others from harm.
Seto's Battle City Deck is very similar to his anime Deck, and it also contains one Level 8 unnamed monster. Dark Marik described his Deck during his Duel with Yugi as a Power Deck designed to suppress the opponent with monsters while gathering sacrifices to Summon his God card. Kaiba is not limited to using his own monsters, however, making liberal use of "Soul Exchange" to use his opponent's monsters as the sacrifices he needed. At the same time, he did not abandon his "Blue-Eyes White Dragons," often using them as either backup or a temporary replacement for "Obelisk," and including multiple methods to Summon them with the utilization of the ordinary twin-Tribute method. He also retained his Virus strategies, which he used against Ishizu, but he likely temporarily abandoned them in the manga after learning that his "Crush Card" strategy would be ineffective against "Ra."
Kaiba runs a Crack-and-Power Deck. Having lost his God card, Kaiba has expanded upon his previous strategies; he includes new support for Virus Cards and also more "self-fusing" Fusion Monsters, notably the "Material" series. His "Blue-Eyes White Dragons" are back to their old position of spearheading his Deck.
A Monster Spirit named Kaibaman—who was rumored to have been created in honor of Kaiba, has been shown to possess a Deck based on Kaiba's Blue-Eyes White Dragon Deck. All the listed cards were part of Kaibaman's Deck.