Todd Snap (トオル Tooru?), a Pokémon photographer, is summoned by Professor Oak to an unusual island to help him with a report. Oak needs quality pictures to accompany his scientific findings, and knows from past experience that Todd is the right person for the job. Pokémon Island, which contains a variety of climatic and geographic regions, is a place where Pokémon live relatively undisturbed by humans. Using a motorized, amphibious buggy named the Zero-One, Todd explores the island and takes photographs of the wide variety of Pokémon that inhabit its environments.

From Professor Oak's research hub, the player can select between the game's levels and features using a menu system. The path through the levels is linear, similar to a rail shooter. Up to 60 pictures can be taken per visit to a course. After completing a course, the player selects their best picture of each Pokémon to be rated by Professor Oak and added to the Pokémon Report. Scoring takes into account various aspects of the pictures, such as the Pokémon's size, its pose, and keeping the Pokémon in frame. Extra points are awarded for capturing a "special" pose or Pokémon, such as a surfing Pikachu, and if there are multiples of the same Pokémon within the frame. Scoring well in the Pokémon Report and photographing a wide variety of Pokémon is required to make progress in the game.

The game features seven levels: Beach, Tunnel, Volcano, River, Cave, Valley, and the special course "Rainbow Cloud." However, the staggered acquisition of items from Professor Oak ensures that the player must re-explore the courses to discover new material. Levels must be replayed in order to locate hidden Pokémon, alternate routes, or photographic opportunities that yield the best scores. It also features a number of special items used to obtain better photographs. Players start out with only a camera, then soon gain an apple projectile; this is thrown to either stun Pokémon or attract Pokémon. As they progress, they obtain new items. Next, they gain an item called "Pester Balls", which are able to knock out Pokémon or flush them out of hiding. The Poké-Flute item is used in a variety of ways, such as awakening, irritating, or hatching Pokémon. It can cause Pokémon to dance, and it can play three different songs, resulting in different dances from certain Pokémon. The final item obtained is the Dash Engine, allowing players to go faster than normal. The game also features an "Album mark" where players can mark their favorite pictures to view at a later date or show to friends.