Linklater was born in Houston, Texas, the son of Diane Margaret (née Krieger), who taught at Sam Houston State University, and Charles W. Linklater, III. He attended Huntsville High School in Huntsville, Texas, during grades 9–11, and finished at Bellaire High School in Bellaire, Texas for his senior year. As a teen, Linklater also won a Scholastic Art and Writing Award. Linklater studied at Sam Houston State University (where he also played baseball), until dropping out to work on an off-shore 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 theater in Houston. At this point, Linklater 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, Texas. He was influenced by Martin Scorsese, Robert Bresson, Yasujirō Ozu, Rainer Werner Fassbinder, Josef Von Sternberg, and Carl Theodor Dreyer. He enrolled in Austin Community College in the fall of 1984 to study film. Since his early 20s, Linklater has been a vegetarian. In 2015, he explained the dietary lifestyle in a Boyhood-style documentary for PETA.