Eagleman was born in New Mexico to Arthur and Cirel Egelman, a physician and biology teacher, respectively. Eagleman decided to change his name from Egelman after discovering alternative spellings in personal genealogy research. An early experience of falling from a roof raised his interest in understanding the neural basis of time perception. He attended the Albuquerque Academy for high school. As an undergraduate at Rice University, he majored in British and American literature. He spent his junior year abroad at Oxford University and graduated from Rice in 1993. He earned his PhD in Neuroscience at Baylor College of Medicine in 1998, followed by a postdoctoral fellowship at the Salk Institute.