Farenholt entered the Navy as a seaman April 24, 1861, after 3 years in the merchant service. He participated in engagements and battles at Battle of Hatteras Inlet Batteries, Battle of Port Royal, Battle of Fort Pulaski, and numerous others. On October 22, 1862 while serving as a member of the howitzer gun crew aboard , ordinary seaman Farenholt was severely wounded at the Battle of Pocotaligo, South Carolina and was discharged from the Navy. He reentered the U.S. Navy in February, 1863 after recovering and was assigned to the monitor participating in almost daily engagements with defenses of Charleston, South Carolina from April 1863 to April 1864. He participated in the unsuccessful storming party of Fort Sumter in September, 1863. Distinguished service led to his appointment as Acting ensign on August 19, 1864, and he was in command of the mortar schooner attached to the squadron in the Sounds of North Carolina later that year. He also participated in the recapture of Plymouth, North Carolina, and several engagements on the Roanoke, Chowan, and Blackwater rivers as well as the capture of Fort Fisher, North Carolina.