Linklater was born in Houston. He attended Huntsville High School in Huntsville, Texas, during grades 9–11, where he played football coached by Joe Clements as a backup quarterback for the #1 ranked team in the state. For his senior year, he moved to Bellaire High School in Bellaire, Texas, because he was better at baseball than football and Bellaire had a better baseball coach. As a teen he won a Scholastic Art and Writing Award.
Linklater studied at Sam Houston State University in Huntsville, Texas (where he also played baseball), until dropping out to work on an offshore oil rig in the Gulf of Mexico. He frequently read novels on the rig, and upon returning to land, developed a love of film through repeated visits to a repertory cinema in Houston. At that point, he realized he wanted to be a filmmaker. He used his savings to buy a Super-8 camera, a projector, and editing equipment, and moved to Austin.
