Quantum Conundrum is a first-person puzzle platformer. The protagonist is a twelve-year-old boy whose mother regularly sends him to the mansion of her brother Professor Fitz Quadwrangle, because she suspects the genius is lonely. During one of his visits the professor's experiments go wrong and he becomes trapped in a pocket dimension. It is up to the boy to resolve the problem, while Quadwrangle is only able to observe and communicate to provide instructions. The boy travels through the different parts of the mansion and because of his age the perspective is low to the ground, rendering the objects and the rooms much larger.
The boy is initially only able to walk around, jump, and pick up, drag and throw items. After a while he gets access to the Interdimensional Shift Device (IDS) that allows him to switch between dimensions. In the Fluffy dimension everything becomes lighter and easier to pick up. Heavy is the opposite, the weight can cause objects to break and they can obstruct lasers. Slow makes time ten times slower than usual and Reverse Gravity reverses the gravity in the environment. The boy's movement is unaffected, regardless of the chosen dimension. Some rooms have a dimension triggered automatically, while in others capsules need to be gathered first to be able to shift between dimensions. In later parts a quick shift between dimensions is required to solve puzzles. For instance, an object can be picked up and thrown in the Fluffy dimension, and while it is still in the air a switch to Heavy can cause it to break through a surface. Using Slow in that situation allows the boy to throw an object and then jump on top to ride along. Many puzzles also focus on precise platform jumping.