Ys II is the sequel to Ys I: Ancient Ys Vanished, and takes place immediately following the end of the first game. The player controls Adol as he battles his way across the land of Ys. As in the first game, Adol's strength is measured in a typical RPG fashion: He has numerical statistics such as HP, Attack Power, and Defense Power that determine his strength. These stats are increased by raising his experience level through battling.

Also returning from the first game is the 'bump' combat system. The player attacks enemies by running into them, and the enemy takes damage according to Adol's Attack Power. A new addition to Ys II is the Magic system: Adol can acquire several different spells he can use throughout the course of play, such as a Fire spell for attack, and a Time spell which can stop enemies as long as it is active. The use of magic consumes Adol's MP stat.

The soundtrack to Ys II was composed by Yuzo Koshiro, Mieko Ishikawa, and Hideya Nagata.