Under the Secretary, the Chief Clerk exercised substantial power over Smithsonian administration, supervising the work of numerous subordinates. On occasion the Chief Clerk even served as Acting Secretary. However, in 1891 Secretary Samuel P. Langley decided to assign the Chief Clerk's duties to others, and the office ceased to exist until it was revived in 1907.

William Jones Rhees served from 1855 to 1891. The office's functions were then performed by other officials: W. C. Winlock, Assistant for Office and Exchanges, 1891-1896; Richard Rathbun, Assistant Secretary in charge of Office and Exchanges, 1896-1901; and F. W. Hodge, Assistant for Office and Exchanges, 1901-1907. Harry W. Dorsey served as Chief Clerk from 1907 until 1933, when the office was again abolished.