The basis of gameplay in Pikmin is to retrieve ship parts by using the three varieties of Pikmin available in different combinations. Olimar discovers multi-coloured plant-animal hybrids that willingly follow his orders and help him recover ship parts. All three of the Pikmin colors that Captain Olimar discovers must be used in order to overcome various obstacles and complete the game. The Pikmin creatures come in three different varieties - red, yellow, and blue. Red Pikmin are the basic type, though more powerful than the other two varieties and resistant to fire. Yellow Pikmin can be thrown higher than the other two and can carry explosives called "bomb rocks", while blue Pikmin are the only ones that can survive in water. They are utilized in various tasks, including carrying objects and enemies, breaking down walls, and defeating enemies. Objects that can be carried vary between ship parts, enemy corpses, and pellets. Only 100 pikmin can follow Olimar at a time.

Time in the game is divided into 30 days. With the exception of the first day, which lasts until the player finds the first ship part, all days in the game are about 13 minutes in length. By the end of each day, all Pikmin should be immediately rounded up, work halted, and Olimar must return with the Pikmin to the ship. The reason for this is that many of the creatures which inhabit the Pikmin's planet are nocturnal predators and eat all Pikmin that are left behind on the surface after the sun sets. If Olimar doesn't collect all 25 mandatory ship parts within this 30 day time limit, his ship's life support systems will fail and Olimar will die from oxygen poisoning. If he does find the parts, then he blasts off into space successfully and returns home.

Apart from the main gameplay, Pikmin also contains a Challenge mode that is unlocked once Olimar gets all three types of Pikmin. Each of the five levels in the main game are available for play. The object of Challenge mode is to grow the greatest number of Pikmin in one day as is possible.

In Pikmin, the main character is Captain Olimar, a tiny extraterrestrial from the planet Hocotate. The story starts when Olimar is taking an intergalactic vacation in outer space. However, during his flight, a comet hits his spaceship, the S.S. Dolphin (a reference to the Nintendo GameCube's codename, "Project Dolphin"), which is then pulled into the gravity field of an uncharted planet. Parts of the spaceship fall off as it plummets to the ground and crashes.

When he regains consciousness, Olimar finds out that the planet's atmosphere contains high levels of oxygen- an element deadly to his people- and he can stay on the planet for only 30 days before his life support system stops functioning. Olimar must retrieve many of the spaceship parts so he can rebuild his spaceship and return to Hocotate. Although Olimar initially states in his journal entries that he needs all 30 parts, as the game moves on it is hinted at that some parts might not be actually necessary to lift off, and, indeed, one can win the game without said parts.

To help Olimar are indigenous creatures called Pikmin, which are nearly extinct and unable to survive in the environment without his leadership when he arrives. As this element of symbiosis develops, Olimar discovers parts of his ship and travels across the Pikmin Planet, which is assumed to be Earth, albeit with unknown fauna, although, the game is speculated to be taking place in a post-apocalyptic Earth where humans have died out, due to the unknown species, and debris that which humans would use. The game has three endings depending upon how successful the player is.