A waterproof boot assembly provides waterproof boots that can be collapsed and stored in a storage case while not in use. The assembly includes a boot having an upper end, a lower end, and a perimeter wall extending between the upper and lower ends. The perimeter wall defines a hollow body having the upper end being open. The boot is comprised of a waterproof material. A sole has a top side being attached to the lower end. A first pad is coupled to the boot. The first pad is positioned in and lines the hollow body. A second pad is coupled to the first pad such that the first pad is positioned between the boot and the second pad.