The Clerk of Court is appointed by the district court, serving as its executive officer for the complex administrative support for the court's operations. Six men have been Clerk in the Southern District of Texas.

• Christopher Dart, July 1, 1902 to April 28, 1913
• L.C. Masterson, May 3, 1913 to May 7, 1940
• Hal V. Watts, July 1, 1940 to December 15, 1951
• V. Bailey Thomas, December 15, 1951 to December 28, 1979
• Jesse E. Clark, December 28, 1979 to July 27, 1992
• Michael N. Milby, July 27, 1992 to present