Yu-Gi-Oh! Online: Duel Evolution was a major update from "Yu-Gi-Oh! Online", that changed many aspects of the game. Players now have their own avatars and can explore portions of Domino City from the original Yu-Gi-Oh! series and the Duel Academy from the Yu-Gi-Oh! GX series. The dueling screen and the Deck editor have also been redesigned and improved.

One of the latest improvements of this game are the NPCs. They exist in both Domino City and Duel Academy. NPCs are both characters that are featured in the series such as Yami Yugi, Seto Kaiba, Jaden Yuki, Alexis Rhodes and characters that aren't featured in the series.

In December of 2009, a new version called Yu-Gi-Oh! Online 3: Duel Accelerator replaced Duel Evolution, making it defunct.