Unlike most of Konami's Bemani series, the Pop'n Music interface is not designed to represent any actual musical instrument. Instead, it uses nine buttons, each three-and-a-half-inches in diameter, laid out in two rows. Five buttons are the bottom row, the other four being the top.

Notes (in this game called "Pop-kun" (ポップ君) and anthropomorphised with faces), which are colour coded depending on position on the controller, fall from the top of the screen. When a note reaches the red line at the bottom of the screen, the player presses the button, which triggers a sound within the song.

When a note is played an accuracy rating is displayed, either “Cool”, “Great”, “Good”, “Bad” or “Miss”. How well you hit a note will determine the effect on your life bar, which must be in the orange zone at the end of the song to clear the stage.