The gameplay in Galaga '90 is built upon the same premise as that of the original Galaga, but is in many ways more complex and more difficult. The game is divided into a series of worlds, each with three stages. The player's ship warps between stages and worlds, and it has the ability to warp to alternate dimensions as well.
There are six Challenging Stages in the game. Each Challenging Stage begins with the on-screen announcement "That's Galactic Dancin'", and each stage has its own music that the enemies "dance" to. The enemies and movement patterns vary depending on the stage and the current dimension. As in Galaga, the objective is to destroy all forty enemies before they leave the playfield.