Legend of Xanadu II continues the story of the first game. Once again, the player controls the adventurer Areios, who emerged victorious after the final battle in the end of the first game. Together with his friend Daimos, Areios is looking for their other friend, who has disappeared. On the way, their ship is attacked by the evil Dragon Riders. It seems the search won't be as easy as they have thought, as Areios gets involved in a dangerous adventure again.

The sequel is very similar to the first game gameplay-wise. The player explores towns, vast outdoor areas, and dungeons, engaging enemies in real-time combat. Damage is inflicted upon the enemies simply by running into them, without any special attack button. There are various weapons to equip, and they level up in proficiency the more the player uses them. Areios gains additional hit points depending on the damage he receives. Party members help him in battles, controlled by the AI. The day and night cycle of the previous game has been removed.

Like in the previous game, there are side-scrolling segments which lead to boss battles at the end of each chapter. Compared to the first game, these stages are noticeably shorter, each containing only the boss fight itself, omitting platforming sections with regular enemies. Bosses must be fought using conventional action gameplay, attacking by pressing a button and jumping to avoid their attacks. It is also possible to defend actively and perform attacks in different directions. The player may opt to fight the bosses alone or select one of the available companions, either AI-controlled or in two-player mode.