Negishi was born in Xinjing (today known as Changchun), the capital of Manchukuo, in July 1935. Following the transfer of his father who worked at the South Manchuria Railway in 1936, he moved to Harbin, and lived eight years there. In 1943, when he was nine, the Negishi family moved to Incheon, and a year later to Kyongsong Prefecture (now Seoul), both in Japanese-occupied Korea. In November 1945, three months after World War II ended, they moved to Japan. Since he excelled as a student, a year ahead of what would have been his graduation from grammar school, he was admitted to an elite secondary school, Shonan High School. At the age of 17, he gained admission to the University of Tokyo. After graduation from the University of Tokyo in 1958, Negishi did his internship at Teijin, where he conducted research on polymer chemistry. Later, he continued his studies in the United States after having won a Fulbright Scholarship and obtained his Ph.D. from the University of Pennsylvania in 1963, under the supervision of professor Allan R. Day.