Heller was born on May 1, 1923 in Coney Island in Brooklyn, New York, the son of poor Jewish parents, Lena and Isaac Donald Heller, from Russia. Even as a child, he loved to write; as a teenager, he wrote a story about the Russian invasion of Finland and sent it to the New York Daily News, which rejected it. After graduating from Abraham Lincoln High School in 1941, Heller spent the next year working as a blacksmith's apprentice, a messenger boy, and a filing clerk.
In 1942, at age 19, he joined the U.S. Army Air Corps. Two years later he was sent to the Italian Front, where he flew 60 combat missions as a B-25 bombardier. His unit was the 488th Bombardment Squadron, 340th Bomb Group, 12th Air Force. Heller later remembered the war as "fun in the beginning. You got the feeling that there was something glorious about it. On his return home he "felt like a hero ... People think it quite remarkable that I was in combat in an airplane and I flew sixty missions even though I tell them that the missions were largely milk runs.
After the war, Heller studied English at the University of Southern California and then New York University on the G.I. Bill, graduating from the latter institution in 1948. In 1949, he received his M.A. in English from Columbia University. Following his graduation from Columbia, he spent a year as a Fulbright scholar in St Catherine's College, Oxford before teaching composition at Pennsylvania State University for two years (1950–52). He then briefly worked for Time Inc., before taking a job as a copywriter at a small advertising agency, where he worked alongside future novelist Mary Higgins Clark. At home, Heller wrote. He was first published in 1948, when The Atlantic ran one of his short stories. The story nearly won the "Atlantic First".
While sitting at home one morning in 1953, Heller thought of the lines, "It was love at first sight. The first time he saw the chaplain, Rosarian fell madly in love with him." Within the next day, he began to envision the story that could result from this beginning, and invented the characters, the plot, and the tone that the story would eventually take. Within a week, he had finished the first chapter and sent it to his agent. He did not do any more writing for the next year, as he planned the rest of the story. The initial chapter was published in 1955 as "Catch-18", in Issue 7 of New World Writing.