Like its predecessor, Dr. Mario 64 is a falling block tile-matching video game. The playing field is represented on-screen as a medicine bottle populated with viruses of three colors: red, blue, and yellow. The main objective of the game to clear the playing field of all the viruses using two-colored medical capsules dropped into the bottle. The player manipulates the capsules as they fall, moving them left or right and rotating such that they are positioned alongside the viruses and any existing capsules. When four or more capsule halves or viruses of the same colour are aligned in horizontal or vertical configurations, they are removed from play. The player receives a game over if the playing field fills up with capsules such that they obstruct the bottle's narrow neck. Points are awarded when viruses are destroyed.
There are several single-player modes present in the game:
Classic - This mode features a similar set-up and design to the original Dr. Mario game.
Story - In this mode, the player may take control of either Dr. Mario or Wario to track down the stolen Megavitamins, battling computer players on the way.
Vs. Computer - In this mode, the player may battle against the computer as any character the player has played as or fought against.
Flash - In this mode, the player must eliminate three particular flashing viruses faster than the computer can.
Marathon - This mode consists of a never-ending rising field of viruses which does not end until the player quits or loses.
Score Attack - In this mode, the player is given three minutes to clear all of the viruses as well as get a high score.
A multiplayer mode also allows up to four players to compete at once in Classic, Flash, or Score Attack gameplay.