O'Neill was born in Brooklyn, New York on February 6, 1927, to Edward Gerard O'Neill, a lawyer, and Dorothy Lewis O'Neill (née Kitchen). He had no siblings. His family moved to Speculator, New York when his father temporarily retired for health reasons. For high school, O'Neill attended Newburgh Free Academy in Newburgh, New York. While he was a student there he edited the school newspaper and took a job as a news broadcaster at a local radio station. He graduated in 1944, during World War II, and enlisted in the United States Navy on his 17th birthday. The Navy trained him as a radar technician, which sparked his interest in science.