Like its predecessor, DuckTales 2 is non-linear and allows the player to choose and complete all levels in any particular order. The controls are almost exactly the same. The only difference is that the player only needs to hold the B button to do a cane bounce rather than holding the down button additionally.
Unlike the first game, the player can return to a level that has already been completed to collect more money and items. In addition, upgrades for Scrooge's cane can be obtained from Gyro Gearloose to grant the player access to new and hidden areas in each level. When a level is completed, the player can visit a store to buy recovery items, extra lives, and other such items using any money the player has collected.
In addition to the unique treasures, each stage has a piece of the map that is hidden in a treasure chest. Locating all of the map pieces is not required to complete the game, but collecting all of them opens up an optional sixth stage in which the lost treasure of McDuck can be found.