The Manchuria Empire was set up by Japan and was ruled substantially by Japanese bureaucrats, who, like ones of the British Empire, had their sons return to Japan for education. Abe was sent back to Tokyo to attend Sejo Koko High School, a famous private school. He was later admitted to the school of medicine of Tokyo University. In 1944, when he heard that Japan would lose the war, and he forged a medical certificate to get home to Manchuria.

Japan's defeat dissolved the Manchurian Empire. The ensuing disorder near the end of 1946 found Abe's father wandering Manchuria attempting to get back to Japan, but a bout of cholera proved fatal.

Abe then moved to Hokkaido, his father's hometown, but soon after went back to Tokyo to finish studying medicine the next year. Abe began experimenting at this time with a variety of radical social and artistic theories. He joined a small literary/artistic/philosophical group called Yoru no kai (Night Association), and soon after his introduction to its leader, philosopher Hanada Kiyoteru, Abe joined the Japanese Communist Party (along with most of the rest of Japan's intelligentsia) and began experimenting with Marxism and surrealism in his literature. Unfortunately, very little of Abe's work from this period has been translated into English, but Abe's youth and idealism comes through clearly in what are some of his most (blackly) humorous and outspoken works. Abe also befriended many avant-garde artists and writers, including some well-known Marxists such as Okamoto Taro, Tesigawara Hirosi, Haniya Yutaka, and Hanada Kiyoteru. It was during this period that he also married Yamada Matiko, who was later known as Abe Mati, a theater artist and designer all of Abe's plays and book covers. Abe also became the pupil of Jun Ishikawa, who was strongly against Marxism.

In 1947, Abe published his first work, a collection of poems, written in 1943 in memory of his father and his friends who died in Manchuria. He printed 50 copies of Mumei Sishu (Anonymous Poems) on a cheap mimeograph at his own expense.

Within a year, Abe graduated from medical school but did not become a doctor (the rumor is he graduated only because he promised never to practice medicine). Instead, he became an author, and published his first novel, The Road Sign at the End of the Street. The work was based on the life of his best friend, Kanayama Tokio, who had run away from home and died in the Manchuria desert.

In 1951, Abe received the most important Japanese literary prize, the Akutagawa Award, for his novel The Crime of Mr. S. Karuma. In 1960 his novel The Woman in the Dunes won the Yomiuri Prize for Literature. It was made into a film by Hiroshi Teshigahara in 1963 and won the jury prize at the Cannes Film Festival. Teshigahara also made The Face of Another into a film.