Mark Lilla was born in Detroit, Michigan in 1956. After briefly attending Wayne State University Lilla graduated from the University of Michigan in 1978 with a degree in economics and political science. While attending Harvard's John F. Kennedy School of Government he began writing journalism, and after graduating in 1980 with a Master of Public Policy, he became an editor of the public policy quarterly The Public Interest, where he remained until 1984. Returning to Harvard, he worked with sociologist Daniel Bell and political theorists Judith Shklar and Harvey Mansfield, receiving his PhD in Government in 1990. His daughter, Sophie Marie Lilla, was born in 1994.

The recurring theme of Lilla's writings is the contested heritage of the modern Enlightenment, especially regarding politics and religion. His first book, G.B. Vico: The Making of an Anti-Modern examines an early figure in the European Counter-Enlightenment, and has an affinity with the works of Isaiah Berlin. (With Ronald Dworkin and Robert B. Silvers, he edited the memorial volume, The Legacy of Isaiah Berlin in 2001). In the 1990s he wrote widely on twentieth-century European philosophy, editing with Thomas Pavel the New French Thought series at Princeton University Press, and writing The Reckless Mind, a meditation on the "philotyrannical" bent of twentieth-century continental philosophy. In recent years he has concentrated on theology and politics, publishing a wide-ranging study of modern political theology, The Stillborn God, based on the Carlyle Lectures delivered at Oxford University in 2003. The book was named one of the "100 best books of the year" by The New York Times Book Review and one of the 150 best books of the year by Publisher's Weekly