The third season of Yu-Gi-Oh! 5D's lasts from episodes 65 to 92. Following the battle with the Dark Signers, the city is reformed and turbo dueling has changed, but a new threat looms, as the 3 Emperors of Yliaster come into play. This season uses two pieces of theme music. The opening theme is "Freedom" by La Vie, while the ending theme is "O-Zone" by Vistlip. Certain episodes also use the insert song "You Say" by La Vie.

The fourth season of Yu-Gi-Oh! 5D's lasts from episodes 93 to 134. As the WRGP begins, the 3 Emperors of Yliaster begin to make their move. The show uses seven pieces of theme music. For episodes 93 through 103, the opening theme is "Freedom" by La Vie, while the ending theme is 'O-Zone' by Vistlip. For episodes 104 to 129, the opening theme is "BELIEVE IN NEXUS" by Masaaki Endoh, while the ending theme is "Close to You" by Alvino ~Alchemy vision normal~. For episodes 130 to 154, the opening theme is "Road to Tomorrow - Going My Way!" by Masaaki Endoh, while the ending theme is "Future Colors" by Plastic Tree. Certain episodes use the insert song: "Clear Mind" by Masaaki Endoh.