Saishu Shiken Kujira's gameplay requires little interaction from the player as most of the game's duration is spent reading the text that appears on the game screen, which represents either dialogue between the various characters or the inner thoughts of the protagonist. After progressing through the text, the player will come to a "decision point" where he or she must choose from multiple options. The time between these decision points varies. Gameplay pauses at these points and depending on which choice the player makes, the plot will progress in a specific direction. With the consumer ports, if an undesired choice was selected, there would be an option to rewind the story to correct the mistake. However, if the player reaches a bad end to a storyline, the player does not have this option and must reload the game at the last saved point.

Saishu Shiken Kujira's gameplay requires little interaction from the player as most of the game's duration is spent reading the text that appears on the game screen, which represents either dialogue between the various characters or the inner thoughts of the protagonist. After progressing through the text, the player will come to a "decision point" where he or she must choose from multiple options. The time between these decision points varies. Gameplay pauses at these points and depending on which choice the player makes, the plot will progress in a specific direction. With the consumer ports, if an undesired choice was selected, there would be an option to rewind the story to correct the mistake. However, if the player reaches a bad end to a storyline, the player does not have this option and must reload the game at the last saved point.