The Ultimate Haunted House places the player in the middle of a bizarrely humorous and eerie haunted house populated by Wilson's wacky characters. The player must explore 13 rooms and find 13 hidden keys before 13 hours on the mystery clock run out.

Gameplay consists of interacting with the a cast of ghoulish residents who populate the house and move about it, and in collecting and exchanging an inventory of items with them. All of the main characters, as well as the house itself, contain artificial personalities that react to the actions of the player; the moody characters and the opportunity to explore the house in any order creates near-infinite replayability. Dozens of activities and puzzles embedded in the game also have consequences. These activities include a monster assembly lab, monster movies in the screening room, cooking a concoction in the kitchen, composing an organ tune, and other traditional puzzle games adapted to the computer. The game contains many clever voices and the opening tune "Monster Mash".