Ernest Everett Just was born on August 14, 1883, in Charleston, South Carolina. to Charles Frazier and Mary Matthews Just.
His father died in 1887 and soon after the Just family moved to James Island, off the coast of South Carolina. His early education consisted of attending the small school that his mother founded and directed. Just left James Island at the age of twelve to attend what is now South Carolina State College. In 1899, Just graduated at age 15 with a certification allowing him to teach in any black school in SC. An intelligent and inquisitive student, Just was not interested in teaching as a career. So he traveled north and started his studies at Kimball Union Academy in New Hampshire before enrolling at Dartmouth College, studying biology, history, literature, and the classics.