The far-off kingdom of Blobolonia is threatened by an evil emperor. An alien blob escapes from Blobolonia, searching for help, and he crash lands on planet Earth. There he finds a young boy. Help the pair save Blobolonia from the Emperor's tyrannical reign!

A Boy and his Blob is based on David Crane's Nintendo game of the same name. As the nameless Boy, you have control over an alien blob who can transform into different objects when you feed him different flavored jellybeans. The transformations are usually based on puns (for example, punch is a hole, apple is a jack and licorice is a ladder) or similar sounding names (such as tangerine trampoline and pear parachute). Using the different tools that Blob can transform into, it's up to the player to reach the exit door at the end of each level.

Each level also has three hidden treasure chests in it. If all three are found, a bonus level is unlocked. The bonus levels are Challenge Levels, which are more difficult, and often based around using a specific skill or jellybean flavor. Completing these levels unlocks special rewards such as concept art, videos and new game modes.