From April 25, 1869 to July 20, 1870 Pierrepont served as U.S. Attorney for the Southern District of New York appointed by President Ulysses S. Grant. As U.S. Attorney, he prosecuted Cuban revolutionaries for violation of the Neutrality Act. On Tuesday June 15, 1869, U.S. Attorney Pierrepont arrested and indicted members of the "Cuban Junta", an organization to aid the Cuban Rebellion. Included in the arrests were the "Cuban Junta" President and other members; Jose Moralez Lemus, Wm. O.C. Ryan, Francisco Fesser, and Jose Mora. The "Cuban Junta" on May 1, 1869 had organized a military expedition to fight in the Cuban Rebellion against Spain. Other members of the "Cuban Junta" escaped arrest by the Deputy Marshall Allan. Pierrepont retired as U.S. Attorney and resumed his private law practice.