Brandon Vera is of Filipino descent, the son of a Filipino father, Ernesto, and his Filipino step-mother, Amelia. His birth mother is Italian-American and was not involved in most of his upbringing. Vera grew up in a family with three brothers and one sister. He also has two other brothers and another sister outside of the family in which he was raised and they were occasionally involved in his life. Vera was born and raised in Norfolk, Virginia, and attended Lake Taylor High School where he excelled in wrestling and earned a four-year athletic scholarship to Old Dominion University. However, he dropped out of Old Dominion after a year and a half when he felt college was not for him, and enlisted himself in the United States Air Force. In the Air Force, Vera joined the wrestling team and trained at the United States Olympic Training Center in Colorado Springs, Colorado. His military wrestling career was cut short in 1999 when he tore ligaments in his right elbow. Arthroscopic surgery repaired the ligaments, but he had nerve damage from the experience, causing him to be unable to use his right arm. He was released from the Air Force on a medical discharge.
Vera returned to Virginia where he steadily rehabilitated his arm, and eventually was fit enough to enter the Grapplers Quest submission wrestling competitions on the East Coast. There, his solitary training methods (he did not belong to a camp and trained and cut weight on his own) caught the attention of Lloyd Irvin, a Brazilian jiu-jitsu Black Belt and coach, who invited him to train with his school. At Irvin's school, he was introduced to mixed martial arts.