Elion was born in New York City on January 23, 1918, to parents Robert Elion, a Lithuanian Jewish immigrant and a dentist, and Bertha Cohen, a Polish Jewish immigrant. Her family lost their wealth after the Wall Street Crash of 1929. Elion was an excellent student who graduated from Walton High School at the age of 15. When she was 15, her grandfather died of stomach cancer, and being with him during his last moments inspired the multi talented Gertrude to pursue a career in science and medicine in college. She was Phi Beta Kappa at Hunter College, which she was able to attend for free due to her grades, graduating summa cum laude in 1937 with a degree in chemistry. Unable to find a paying research job after graduating because she was female, Gertrude worked as a secretary and high school teacher before working in an unpaid position at a chemistry lab. Eventually, she saved up enough money to attend New York University and she earned her M.Sc. in 1941, while working as a high school teacher during the day. In an interview after receiving her Nobel Prize, she stated that she believed the sole reason she was able to further her education as a young female was because she was able to attend Hunter College for free. Her fifteen financial aid applications for graduate school were turned down due to gender bias, so she enrolled in a secretarial school, where she attended only six weeks before she found a job.