The game took the one-man development team, Daisuke Amaya, five years to make.

Right after the fight with Curly Brace, you can go into her room. In there, you can find a secret tunnel. At the end, you will find an item called "Curly's Underwear." This item is a joke item, as it has no use and cannot be removed from your inventory.

There is a portrait image of Sue as a human within the game. This is never used, but it suggests that sometime during development, Sue, in her human form, had dialog.

In late 2011, a .zip file was uploaded to the Doukutsu Uploader that contained all 19 versions of orgview made throughout Cave Story's development timeline. Dozens of different beta versions of songs that play in-game, including some unused ones in the final version, were part of the package.