Fusion Deck is the antiquated term for what is now the Extra Deck, however the term is still printed on many old cards, and in most Video Games. The Fusion Deck could only store Fusion Monsters during a Duel. They were separate from the Main Deck, and you could search through it to find a Fusion Monster that you needed. There was no limit as to how many cards you could use in the Fusion Deck, although some Video Games enforced a 15-card limit. The "Maximum of 3 Rule", for cards of the same name still applied.

If a Fusion Monster on the field, in the Graveyard or Removed from Play was returned to its owner's hand or Deck, it is instead sent to the Fusion Deck, since Fusion Monsters could not exist in either the hand or the Main Deck.

The contents of the Fusion Deck are not public knowledge to your opponent, and only you may look through its contents.