He attended Music and Arts high school in Newark, and graduated as an art major; his music interests were limited in those days. Near the end of his high school career he picked up a saxophone, and with the encouragement of his father began to play."For awhile I would listen to with just half an ear, simply to please my father. Then one day on the radio, I heard a Thelonius Monk composition with Art Blakey on drums. That was when I began listening and thinking seriuosly about music."

Upon graduation from NYU in 1956 he was drafted and served in the US Army until 1958. During his stint in the army he was able to play a three-night gig in Philadelphia with Horace Silver's quintet. After his discharge from the army, he was back in New York and played a short time with Maynard Ferguson. It was here that he met pianist Joe Zawinul, with whom he would later found Weather Report.

Shorter joined Art Blakey's Jazz Messengers in 1959 and was with them until 1963. During his stint with the Messengers he was joined by trumpeter Lee Morgan, pianist Bobby Timmons, bassist Jymie Merritt, and Blakey. During this time with the Messengers he also became the "musical director" of the band, as had Horace Silver and Benny Golson before him. It was also during this time that he made his first recordings as a leader on the Chicago-based Vee-Jay label.

1964 was a giant year in Shorter's career. He made his debut as a leader on Blue Note Records (Night Dreamer), and joined the Miles Davis Qunitet in place of the departed John Coltrane. This had to be a bittersweet experience for Shorter, replacing one of the men whom he cites as a major influence on his playing style. Many people feel that Shorter's playing style in his early years was influenced by both Coltrane and Sonny Rollins. Others would say that is original and not derivative. All would probably agree that it is outstanding whether original or derived.

When Shorter joined the Miles Davis quintet, Davis would later write; 'when he (Shorter) came into the band it started to grow a lot more, and a whole lot faster, because Wayne is a real composer. He writes scores, write the parts for everybody just as he wants them to sound. He also brought in a kind of curiosity about working with musical rules. If they didn't work, then he broke them, but with musical sense; he understood that freedom in music was the ability to know the rules in order to bend them to your own satisfaction and taste."

During Shorter's time with Davis he composed such songs as "Footprints", "ESP", "Nefertiti", "Pinocchio", and "Deloris" which have become jazz standards. Also during this time the Davis quintet began to move away from the bop formula of quick and jumpy on the top and a stable pulse on the bottom, to stability on the top and rythmic complexity on the bottom. Shorter would later use this formula in Weather Report.