Black Jack: Hi no Tori Hen is very much a Elite Beat Agents-style game, having to tap or drag your stylus across the screen at the right speed and accuracy, as well as a comic to read in the background of the game to be used a storyline for each patient, some have an effect of what happens during surgery causing distractions or harder accuracy.

For most of the game, Black Jack is just simply performing surgeries for Tezuka's Star System characters, some of which are based on chapters from the Manga series. Though the game has its own main plot as the game progresses.