During the age of the dinosaurs, a massive famine forces several herds of dinosaurs to seek an oasis known as the Great Valley. Among these, a mother in a diminished “longneck” herd gives birth to a single baby, named Littlefoot. Years later, Littlefoot plays with Cera, a “three-horn”, until her father intervenes and tells her that three-horns don’t play with longnecks, whereupon Littlefoot’s mother describes the different kinds of dinosaurs: “three-horns”, “spike-tails”, “swimmers”, and “flyers”. That night, as Littlefoot follows a “hopper”, he encounters Cera again, and they play together briefly until a large “Sharptooth” attacks them. Littlefoot’s mother comes to their rescue, but receives fatal injuries in the process. An earthquake swallows up the Sharptooth and divides Littlefoot and Cera and other dinosaurs from their herds while some die in the process, including Littlefoot’s mother, who gives her son some words of advice about finding the Great Valley before she dies that night. Confused and in grief, Littlefoot meets an old “clubtail” named Rooter, who consoles him. He is then guided by his mother’s voice telling him to follow the sun to the Great Valley and pass several landmarks, such as a rock formation that resembles a Longneck and the “Mountains that Burn”.
Later, Littlefoot meets a “bigmouth” named Ducky and a “flyer” named Petrie, who accompany him on his journey. Cera, who is attempting to find her own kind, finds the unconscious Sharptooth inside a ravine and mistakenly wakes him up. She escapes and bumps into Littlefoot, Ducky, and Petrie; she tells them that the Sharptooth is alive and pursuing them, but Littlefoot does not believe her. As Cera describes her encounter, she accidentally flings Ducky to the direction of a lone hatching “spiketail”, whom she names Spike and inducts into the group. Seeking the Great Valley, they discover a cluster of trees, which is abruptly depleted by a herd of Longnecks. Searching for remaining growth, they discover a single leaf-bearing tree, and obtain food by stacking up atop each other and pulling it down. Cera remains aloof, but at nightfall, everyone including herself gravitates to Littlefoot’s side for warmth and companionship.
The next morning, they are attacked by the Sharptooth, but they manage to escape through a tunnel that is too small for him to follow. Beyond this, they discover the landmarks mentioned by Littlefoot’s mother. Cera stubbornly decides to go another way, but Littlefoot, fed up with Cera’s stubbornness, refuses, and their ensuing fight leads to a schism that divides him from the others. However, when Ducky and Spike become endangered by lava, Petrie gets stuck in a tar pit, and Cera gets ambushed by a pack of “domeheads” (Pachycephalosaurus) who are also living in the Mountains that Burn, Littlefoot returns to rescue them. He, along with Ducky, Petrie and Spike, pose as a tar monster, scaring Cera out of her wits. When she realizes who it really is, she storms off in a huff. It is not long, however, until she gives in to her guilt, being that her stubbornness put others in danger for her own selfish desires, and the imagined shame she would receive from her father. Later, while crossing a pond, Petrie overhears the Sharptooth nearby. The group devises a scheme to lure him to the pond and drown him in the deep side using a nearby boulder. During the ensuing struggle, a draft from the Sharptooth’s nostrils enables Petrie to fly for the first time.
The plan nearly fails when the Sharptooth begins attacking the boulder while the group attempts to push it onto him. However, Cera reunites with the group, and she headbutts the boulder, causing the Sharptooth to fall into the water below with the boulder falling on him in the process. The Sharptooth momentarily takes Petrie down with him to his death, but he later emerges unharmed. Littlefoot, alone, follows a cloud resembling his mother, which guides him to the Great Valley. He is then joined by the others. Upon arrival, the five are reunited with their families: Petrie impresses his family with his newfound flight; Ducky introduces Spike to her family, who adopt him; Cera reunites with her father; and Littlefoot rejoins with his grandparents. The group then rejoins at the top of a hill and embrace each other in a hug.