Keller was born in Alsace, France, and graduated from the École Hoteliere in Strasbourg. Beginning as a pastry chef, he worked in various restaurants including Auberge de L'Ill, the cruise liner Mermoz, Domaine de Chateauneuf, and Moulin de Mougins in France, and La Cuisine du Soleil in Sao Paulo, Brazil. He trained under Paul Haeberlin (chef), Paul Bocuse, and Roger Verge before coming to San Francisco in 1982 to revitalize the now-defunct Sutter 500.
In 1986 he became co-owner and executive chef of the original Fleur de Lys in San Francisco. He later opened Burger Bar in Mandalay Bay Resort and Casino in Las Vegas, Nevada, which features a $60 "Rossini Burger" made of American Kobe beef, sautéed foie gras, and shaved truffles. Shortly thereafter he opened a second Fleur de Lys, also at Mandalay Bay. He is the consulting chef at the Club XIX, at the Lodge in Pebble Beach in Pebble Beach, California. He is the author of The Cuisine of Hubert Keller and is the co-author of Dr. Dean Ornish's Eat More, Weigh Less. Keller was the first guest Chef with Jean-Marc Fullsack to cook a dinner for a President (Clinton) in White House history. Hubert appeared three times as a guest judge on the Bravo reality TV show Top Chef in the series premiere, season one finale, and season two finale. In 2008 he was invited in the First Annual Food and Wine Exhibition in Monterey, California.
In 1988 Hubert Keller was ranked as one of the "10 best new chefs in America" by Food & Wine Magazine In 1997 he won the James Beard Foundation award for best chef in California. Fleur de Lys in San Francisco has been ranked as one of the top 40 restaurants in the United States in 2004, 2005, and 2006 by Gayot restaurant guide , and was awarded one Michelin star in 2006. Fleur de Lys has also been ranked as one of the top 25 restaurants in the United States by Food & Wine magazine.