Nathan Jaffee was born in Brooklyn, NY, in 1921. He was the third child of Isidore and Anna Jaffee, who were Russian and Polish Jewish immigrants. They first lived on Georgia Avenue, in Brownsville, before moving to other neighborhoods of Brooklyn, including Bensonhurst and Crown Heights. After his mother died, Jaffee left school and worked as a typesetter and union organizer, before being drafted into service during World War II. He served as an infantry squad leader and saw heavy combat in Europe.

After returning from the war, he began photographing his New York City surroundings, capturing the people and streets of the city. He took classes at the Photo League and studied under Sid Grossman. While working on his photography, he continued to be employed in the printing industry and was active in progressive politics. In 1945, he married Isabel Spector. They had two daughters, Anna and Cyrisse, and moved to Queens. Later, he moved to Huntington, NY, with his companion Paula Hackeling.

His work was part of the 1950 exhibit, "Fifty-One American Photographers," curated by Edward Steichen at the Museum of Modern Art. His work is held by numerous museums and galleries, including the Brooklyn Museum, the Metropolitan Museum of Art, the Smithsonian Institution, the National Portrait Gallery, the Library of Congress, the National Museum of American Art, the New York Public Library, the Brooklyn Public Library, the Bibliotheque Nationale de France, the International Museum of Photography and Film (George Eastman House), the Museum of Fine Arts (Boston), and the Fogg Art Museum at Harvard University. A book of his photographs, N. Jay Jaffee: Photographs 1947–1956, was published in 1976.

N. Jay Jaffee died in 1999. A 50-year posthumous retrospective, "From Coney Island to Caumsett: The Photographic Journey of N. Jay Jaffee, 1947–1997," was shown at the Heckscher Museum in Huntington, NY, later that same year. As of 2023, his work is represented by the N. Jay Jaffee Trust.