Super BurgerTime is a sequel to BurgerTime. The players control Peter Pepper Jr. or his twin brother Pete Pepper Jr. (in two players mode), sons of the protagonist of BurgerTime, as they try to cook burgers. To do so, they have to run through a maze of platforms jumping on the burger's parts (like buns, meat patty, lettuce, etc.) in order to make them fall all to the bottom of the screen, thus assembling them. Bigger parts require more jumps to fall, smaller parts require fewer jumps. If a part standing on a superior platform falls over a part standing on an inferior platform, the part standing on the inferior platform falls from where it stands. A burger is complete when all parts are aligned in the serving plate at the bottom of the screen. A level is complete when all burgers are done.
As Pepper Jr. tries to do his job, foods of all sorts try to stop him. To defend himself, he can use an assortment of weapons. He starts off with a pepper cellar which can be used to throw pepper in those foods, temporarily paralyzing them or later killing them. They re-spawn over time, and the pepper cellar only lasts for a few seconds. Enemies can also be killed by burger parts falling over them. Other weapons are available at the sides of the screen, where towers stand with girls inside them. The girls will leave the weapons hanging to be picked up, as well as items which can help Pepper Jr. (like a cape which makes him invulnerable for one hit).
The game is divided in "worlds", each one comprised of 4 stages. At the end of each world, a boss fight waits Pepper Jr. During these fights, he will use his burgers as weapons, throwing them against the boss until it finally dies.