Cummings was born in Cambridge, Massachusetts, on October 14, 1894, elder of two children to Edward Cummings and Rebecca Haswell Clarke. His younger sister, Elizabeth, was born in 1901.

He was named after his father but his family called him by his middle name, Estlin. His father was a professor of sociology and political science at Harvard University and later a Unitarian minister. Cummings described his father as a person who could accomplish anything that he wanted to. Edward was well skilled and was always working on repairing things. He and his son were close, and Edward was one of Estlin's most ardent supporters.

His mother never partook in stereotypically "feminine" things, and enjoyed reading poetry to her children. Raised in a well-educated family, Cummings was a precocious boy and his mother encouraged Estlin to write poetry every day. He wrote his first poem when he was only three: "Oh,the pretty birdie,O;/with his little toe,toe,toe!"

His boyhood home, the E. E. Cummings House, is located in Cambridge, Massachusetts, and is listed on the National Register of Historic Places.

Cummings enrolled at Harvard University in September 1911, from which he received a Bachelor of Arts degree in 1915, graduating magna cum laude, and in the next year completed his Master's degree in English and Classical Studies also at Harvard. While at Harvard, he befriended John Dos Passos, at one time rooming in Thayer Hall, named after the family of one of his Harvard acquaintances, Scofield Thayer, and not yet a freshman-only dormitory. Several of Cummings' poems were published in the Harvard Monthly as early as his sophomore year. Cummings himself labored on the school newspaper alongside fellow Harvard Aesthetes John Dos Passos and S. Foster Damon. In 1915, his poems were published in the Harvard Advocate.

In his final year at Harvard, Cummings was influenced by writers such as Gertrude Stein and Ezra Pound. He delivered a controversial commencement address to his graduating class entitled "The New Art". This speech gave him his first taste of notoriety, as he managed to give the false impression that the well-liked imagist poet, Amy Lowell, whom he himself admired, was "abnormal". For this, Cummings was chastised in the newspapers. In 1917, Cummings' first published poems appeared in a collection of poetry entitled Eight Harvard Poets.

In 1917 Cummings enlisted in the Norton-Harjes Ambulance Corps, along with his college friend John Dos Passos. Due to an administrative mix-up, Cummings was not assigned to an ambulance unit for five weeks, during which time he stayed in Paris. He fell in love with the city, to which he would return throughout his life.

During their service in the ambulance corp, they had sent letters home that drew the attention of the military censors and preferred the company of French soldiers over fellow ambulance drivers. The two openly expressed anti-war views; Cummings spoke of his lack of hatred for the Germans. On September 21, 1917, just five months after his belated assignment, he and a friend, William Slater Brown were arrested by the French military on suspicion of espionage and undesirable activities. They were held for 3½ months in a concentration camp at the Dépôt de Triage, in La Ferté-Macé, Orne, Normandy.

They were imprisoned with other detainees in a large room. Cummings' father failed to obtain his son's release through diplomatic channels and in December 1917 finally wrote a letter to President Wilson. Cummings was released on December 19, 1917, and Brown was released two months later. Cummings used his prison experience as the basis for his novel, The Enormous Room about which F. Scott Fitzgerald said, "Of all the work by young men who have sprung up since 1920 one book survives...The Enormous Room by e e cummings....Those few who cause books to live have not been able to endure the thought of its mortality."

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