Nathan was born in Providence, Rhode Island. After receiving a master’s degree in French literature from the University of Michigan, she then went on to earn a master’s degree in public administration from Harvard University's John F. Kennedy School of Government. For three years she lived in Israel working for Mayor Teddy Kollek of Jerusalem. She was one of the founders of New York's Ninth Avenue Food Festival under mayor Abraham Beame.
Nathan was also the executive producer and host of Jewish Cooking in America with Joan Nathan, a PBS series based on her cookbook, Jewish Cooking in America.
Most recently, she wrote The New American Cooking, which won the James Beard and IACP Awards for Food of the Americas and Best American Cookbook, respectively. Nathan was also the guest curator of Food Culture USA at the 2005 Smithsonian Folklife Festival, which was based on the research for her book.
She has written a total of ten cookbooks, winning numerous awards for them. Nathan, the mother of three grown children- Daniela, David, and Merissa- lives in Washington, D.C. and Martha's Vineyard with her husband, attorney Allan Gerson.
In January 2009 she was saved from choking to death on a piece of chicken at the Art.Food.Hope dinner in Washington DC by chef Tom Colicchio, who performed the Heimlich maneuver on her.