The position of Deputy Director was created in 1971 when Director Michael Collins appointed Melvin B. Zisfein to the office. Zisfein, who was also Acting Director in 1978, served until 1981 when he left the Museum. Walter J. Boyne was named Deputy Director in 1981 and held the office, along with that of Acting Director, until 1983, when he became Director. In 1983, Boyne chose Donald S. Lopez to be Deputy Director for Curatorial Services. In 1984, the title was shortened to Deputy Director. Lopez served until 1990.

After 1990, Lopez assumed a role as an adviser to the Director until 1995 when he became Acting Director again. In between, Wendy Stephens was named Associate Director from 1990 until 1992. She was followed by Gwendolyn Carter from 1993 until 1995. When Donald Engen was appointed Director of the Museum, Lopez once again assumed the Deputy Director's position where he remains today. He also was Acting Director in 1999 when Engen died in July of that year, until the appointment of John R. Daley as Director of the Museum in January 2000.