Similar to the previous season, The Walking Dead: Season Two is a point-and-click adventure game. The player, in control of Clementine, can direct the character around the environment, examine and interact with various scenery elements and collect and use objects to advance the story. The player can also initiate conversations with non-player characters via conversation trees. Certain replies from other characters may offer the player multiple choices to select from, including the option to stay silent, with a limited amount of time to make the selection; if the player does not select an option, the conversation will continue as if they had stayed quiet. Such choices can affect how the other characters will later react to Clementine which can influence later events in the story. Other scenes are more action-oriented, requiring the player to complete quick time events to avoid Clementine or her allies from getting killed. If the player fails these events, the game will restart at the start of such scenes. Such action scenes may also require the player to make a key decision within a limited time frame, such as which of two characters to save from attacking walkers.

The Walking Dead: Season Two continues the story of Clementine, a young girl orphaned by the undead apocalypse. Left to fend for herself, she has been forced to learn how to survive in a world gone mad.

Many months have passed since the events seen in Season One of The Walking Dead, and Clementine is searching for safety. But what can an ordinary child do to stay alive when the living can be just as bad – and sometimes worse – than the dead? As Clementine, you will be tested by situations and dilemmas that will test your morals and your instinct for survival.