In the fall of 1987, Agee began his freshman year at St. Joseph High School. St. Joseph's is the same school that Arthur's childhood hero, Isiah Thomas, attended. Since the school was an hour and a half from his home, Arthur woke up at around 5:30 AM daily and took public transportation to reach his destination. Early on in his high school career, when his parents were unable to keep up with the school's tuition payments, Agee had to leave St. Joseph's and instead attended John Marshall High School, an inner-city school. In his senior year, he helped the Marshall Commandos win the 1991 Public League Championship and finish third for the State Championship. Agee's high school was defeated by Manual High School that was led by Future NBA player Howard Nathan.

After graduating from Marshall, Agee starred at Mineral Area College and went on to play for two years at Arkansas State on a scholarship. He is a member of Phi Beta Sigma fraternity. Although Agee played at a Division I school, he never achieved his dream of playing in the National Basketball Association. In 1996, Agee turned down a contract with the CBA's Connecticut Pride to take a role in the film Passing Glory. In 2004, he launched a 'Hoop Dreams' clothing line with the slogan "Control Your Destiny". On December 15, 2004, his father, Arthur "Bo" Agee Sr., was killed while attempting to run from at least one robber. A Chicago man was subsequently charged by Berwyn police, but ultimately acquitted of killing Arthur Agee Sr. On November 19, 2017, Agee was arrested and held on $30,000 bail after being charged with aggravated battery for punching a woman in west suburban Forest Park.