3D Fongus is a flight racing game played from a third person perspective. The player flies over a desert where flags create the race track. Controls are limited to turning left and right. The player earns points for each pair of flags he flies through and also for flying over various things such as hedgehogs and cacti. There are also obstacles to watch out for such as rocks and rhinoceros that sometimes walks across the race track. The plane can take some damage but after five hits the game ends.
At some places the player will find holes in the ground that he can fly down into and enter a cavern. Going through a cavern shortens the length of the race and down there it's possible to find wrenches that repairs some of the plane's damage. The cavern is also the place of the yellow fungus which the player has to avoid since contact with it is lethal.