Shelton Jackson Lee was born March 20, 1957, in Atlanta, Georgia to William "Bill" Lee, a jazz composer and bassist, and Jacqueline Shelton Lee, an art teacher. His mother, who died in 1977 of cancer, nicknamed him "Spike" as toddler, evidently alluding to his toughness. Spike grew up the oldest three brothers, David, Cinque, and Chris, and one sister, Joie. The family moved from Atlanta shortly after Lee's birth and lived briefly in Chicago. In 1959 they moved to Brooklyn's predominantly black Fort Greene section. Jacqueline Lee provided a rich cultural upbringing that included plays, galleries, museums, movies. Bill Lee saw that the family experienced music, occasionally taking them to his performances at the Blue Note and to other Manhattan jazz clubs.

After graduating from John Dewey High School in Brooklyn, Lee majored in mass communications at his father's and grandfather's alma mater, Morehouse College in Atlanta. At Morehouse Lee took an interest in filmmaking, and upon graduation in 1979, was awarded a summer internship with Columbia Pictures in Burbank, California. In the fall, he returned to New York to attend New York University's Institute of Film and Television, Tisch School of the Arts. One of the few blacks in the school, Lee's first year at NYU was not without controversy. For his first year project he submitted a ten minute film, The Answer, that told of a young black screenwriter who remade D. W. Griffith's The Birth of a Nation. A pointed critique of the racism in Griffith's silent film, the faculty was displeased with his work, saying that he had not yet mastered "film grammar." Lee suspected, however, that they took offence to his digs at the legendary director's stereotypical portrayals of black characters. An assistantship in his second year provided full tuition in exchange for working in the school's equipment room.

Lee earned his master's in filmmaking from NYU in 1982, and as his final film project, he wrote, produced, and directed Joe's Bed-Stuy Barbershop: We Cut Heads. His father composed the original jazz score, the first of several he created for his son's films. The film was set at a barbershop in Brooklyn's Bedford-Stuyvesant neighborhood that serves as a front for a numbers running operation. The Academy of Motion Picture Arts and Sciences awarded Lee the 1983 Student Academy Award for best director. The Lincoln Center's New Directors and New Films series selected the film as its first student production.

Upon graduation two major talent agencies signed Lee, but when nothing materialized, he was not surprised. In a New York Times interview, Lee said that it "cemented in my mind what I always thought all along: that I would have to go out and do it alone, not rely on anyone else." Even though the honors enhanced his credibility, they did not pay the bills. In order to survive, Lee worked at a movie distribution house cleaning and shipping film.

At the same time, he tried to raise funds to finance a film entitled Messenger, a drama about a young New York City bicycle messenger. However, in the summer of 1984, a dispute between Lee and the Screen Actor's Guild forced a halt in the production of his first film. The Guild felt the film was too commercial to qualify for the waiver granted to low-budget independent films that permitted the use of nonunion actors. Lee felt that the refusal to grant him the waiver was a definite case of racism. Unable to recast the film with union actors, he terminated the project for lack of funds. Lee told Vanity Fair that he had learned his lesson: I saw I made the classic mistakes of a young filmmaker, to be overly ambitious, do something beyond my means and capabilities. Going through the fire just made me more hungry, more determined that I couldn't fail again.

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