Nirenberg was born in New York City to a Jewish family, the son of Minerva (Bykowsky) and Harry Edward Nirenberg, a shirtmaker. He developed rheumatic fever as a boy, so the family moved to Orlando, Florida to take advantage of the subtropical climate. He developed an early interest in biology. In 1948 he received his B.S. degree, and in 1952, a master's degree in zoology from the University of Florida at Gainesville where he was also a member of the Pi Lambda Phi Fraternity. His dissertation for the Master's thesis was an ecological and taxonomic study of caddis flies (Trichoptera). He received his Ph.D. in biochemistry from the University of Michigan, Ann Arbor in 1957, studying hexose uptake in tumor cells with his advisor James F. Hogg.