Girl Genius: The Works is a non-collectible card game that consists of several standalone decks of cards. You can play the game with any one of those decks, while also being able to combine some or all of those decks into a single deck for a longer game or a game with more players. Each deck contains many unique cards, but the gameplay is the same in all cases.

Each player gets a five-card hand and twelve cards are laid out face-down in a patchwork pattern. Each card has colored symbols along each side, as well as a point value and special instructions. On your turn, you reveal one face-down card, then spin any face-up card 180º. After spinning, if any of the symbols on the edges of the spun card match the symbols on one or more of the surrounding cards, you "pop" the card(s) with the most matching symbols. "Popping" a card means that you must follow the instructions on the card (whether helpful or harmful), then (usually) add it to your score pile. Cards in your hand are used to replace any popped cards. The game is played until one player has 70/50/40/30 points with two/three/four/more than four players.

Master Payne's Circus of Adventure contains story elements from Agatha's time in the circus as well as her visit to Sturmhalten. Unique character blocks in this deck include Circus Cards, Mimmoths, and some fairly nasty Villains. Roughly ten cards in this deck are part of Master Payne's traveling circus. Although these Circus Cards have different effects, popping some — such as André and Lars — grant you an automatic win if you have five or more Circus Cards in your score pile!

Many of the other cards are designed specifically to help you get closer to the Circus Card goal. Baba Yaga, for example, lets you steal a Circus Card from another player's score pile. The Horse Monster Beastie, on the other hand, scares all the Circus Cards from play back into the deck!

The Mimmoths — tiny, wooly, adorable mammoths — travel in herds, so whenever you pop one of them, you get to steal all the others from every player's score pile! Though Mimmoths are only worth three points each, there are six of them in the deck, and they can snowball into an 18-point block.