Yugi plays a Strategy Deck, containing various flexible strategies for any situation, however, two Types that can be seen consistently throughout Yugi's Decks are the Fiend-Type and the Spellcaster-type, possibly to reflect Yami's mystical and somewhat dark nature. In later arcs, it becomes increasingly focused on his "Dark Magician" and the Summoning of the Egyptian Gods.
Yugi's Virtual World Deck is largely similar to his Battle City Deck, though he did not have the luxury of his God Cards. He also included several cards he had formerly used in Duelist Kingdom, but not in Battle City. He also introduces new support for his Duelist Kingdom themes, such as "The Rock Spirit" (EARTH monsters) and "Sangan" (low ATK). For his Duel with Noah Kaiba, Yugi would shuffle his Deck together with the remainder of Seto's own.
Yugi plays a Kuriboh/Timaeus Deck during the Waking the Dragons arc, focusing on Summoning the 5 Kuriboh Brothers through "Five Star Twilight" and combining them to form "Kuribabylon" and raising its ATK through "Pump Up" and "The Seal of Orichalcos" (the latter when he was under its influence). He also makes use of his "The Eye of Timaeus" card he received in order to defeat Dartz, by fusing it with his Magicians in order to Summon powerful Fusions. He supports his strategy by using "Excalibur" or "Altar of Restoration". In his Duel against Dartz, he focused on the three "Legendary Knights" to take down his most powerful monsters through their own special abilities or by fusing them into "Timaeus the Knight of Destiny". Because of Yami's loss to Rafael, Yugi's soul was taken and thus he played no part in the Duels for the rest of the season, save a Duel against Yami that acted as a test of the latter's character. Cards used by Yami after this point are listed at Yami Yugi's Decks, as Yugi had no part in any further alterations to the Deck.
In the movie, Yugi's Deck adds more support for his "Dark Magicians" as well as a higher amount of resources devoted to Summoning the God cards. Only the cards used by Yugi in his Duel were shown in the film, but the full Decklist (totaling out to exactly forty cards) was given in the novelization of the film.
In Yu-Gi-Oh! GX, Yugi's Deck featured cards that he had previously used in a variety of arcs, including some not seen in a while. The Duel between him and Jaden Yuki is known to have taken place sometime after a second version of Battle City.