The opening slideshow shows the titular character, Frogger, listening in on a conversation between two young boys (Blair and Gavin) fishing by a lake. They discuss the classic fairy tale staple of a princess' kiss having the magical property of turning a plain frog into a handsome prince. Upon hearing this, Frogger decides to seek out a princess willing to kiss him. Subsequently, the progression of this quest is presented in the form of slideshows played in between certain stages. They show Frogger's encounters with a variety of characters, who provide him with advice, or ask him to solve certain tasks.
Frogger Advance features traditional 2D side-scrolling platforming mechanics rather than the top-down gameplay of the original Frogger arcade game. The player's primary objective is simply to reach the end of each stage, overcoming the obstacles and enemies in their path by means of jumping, or attacking. This is made easier by Frogger's special abilities, which he is granted at predetermined points throughout the game by a recurring frog fairy character. These abilities include the Super Tongue (a more powerful close range attack), Glide, Double Jump, and an underwater forward thrust.
The game is divided into four different worlds (or chapters), each of which consist of three regular stages and one special stage featuring a boss character, or a special task, which has to be completed within a time limit. Upon completion of each of these worlds, the player's performance is graded in a range from A+ to F- according to three criteria: how many coins were collected, how many hidden gems were found and how many lives were lost. If the player manages to complete the entire game with A+ grades in all worlds, a special, more conclusive ending slideshow is played.