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Lewis was born in Little Rock, Arkansas. His father, John Henry Lewis, Sr., graduated from Yale University School of Divinity and received an M.A. in sociology from the University of Chicago, and was principal of . His mother taught high school math. Lewis attended parochial school in Little Rock, then Wilberforce Preparatory School and Xenia High School in Ohio. When the family moved to Atlanta, Georgia, Lewis attended Booker T. Washington High School until his early admission on scholarship to Fisk University in Nashville, Tennessee. He graduated Phi Beta Kappa in 1956.

Lewis briefly attended the University of Michigan Law School, then transferred to Columbia University where he earned his M.A. in history in 1959. In 1962, Lewis was awarded a Ph.D. in modern European and French history from the London School of Economics.

In 1961-1962, Lewis served in the United States Army as a psychiatric technician and private first class in Landstuhl, Germany.

In 1963, he lectured on medieval history at the University of Ghana. Lewis taught at Morgan State University, the University of Notre Dame, Howard University, University of California at San Diego and Harvard University before joining Rutgers University in 1985 as the Martin Luther King Jr. Professor of History. Lewis produced his Pulitzer Prize-winning biographies of W. E. B. Du Bois during his 18-year tenure at Rutgers. In 2003, Lewis was appointed and is currently the Julius Silver University Professor and Professor of History at New York University.

Lewis is the author of the first academic biography of Martin Luther King, Jr., appearing less than two years after the subject's assassination. Besides the two Pulitzer Prizes for his biographies of W. E. B. Du Bois, he is also the 1994 winner of the Bancroft Prize and the Francis Parkman Prize. He has received fellowships from the Center for Advanced Study of Behavioral Sciences, the National Humanities Center, the Woodrow Wilson International Center for Scholars, the John Simon Guggenheim Foundation, the American Philosophical Society, and the John D. and Catherine T. MacArthur Foundation. He is a former trustee of the National Humanities Center, former commissioner of the National Portrait Gallery, and a former senator of Phi Beta Kappa.

Lewis was president of the Society of American Historians in 2002, and is a board member of the magazine The Crisis, published by the NAACP. He is a fellow of the American Academy of Arts and Sciences and the American Philosophical Society. and was an Ellen Maria Gorrissen Fellow at the American Academy in Berlin, Germany, in spring 2008. President Barack Obama awarded the 2009 National Humanities Medal at the White House on February 25, 2010.

Dr. Lewis lives in Manhattan and Stanfordville, New York with his wife, Ruth Ann Stewart, Clinical Professor of Public Policy at New York University. Dr. Lewis has three adult children from his first marriage to Sharon Lynn Siskind: Eric Levering Lewis, Allison Lillian Lewis and Jason Bradwell Lewis along with a son-in-law Michael John Wilson and two granddaughters Marissa Lynn Wilson and Natalie Elise Wilson. Lewis also has a stepdaughter, Allegra Stewart. He is a convert to Islam.