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Woolsey, the son of Commodore Melancthon Taylor Woolsey, was born at Sackett's Harbor, New York. He entered the Navy as a midshipman on 24 September 1832. After duty at sea and a tour at the Naval School, Woolsey became a passed midshipman on 16 July 1840. He progressed through the rank of master to that of lieutenant by 1847. It was in that rank that he was placed on the reserve list by the retiring board in September 1855. Lt. Woolsey returned to active duty in 1861 as a result of the Civil War.

Assigned initially to the receiving ship at New York, Woolsey had assumed command of the steamer Ellen by late 1861 and began patrol duty with the South Atlantic Blockading Squadron. During that tour, his ship fought Confederate forces on three separate occasions. In May 1862, he engaged Fort Pemberton at Wapper Creek, South Carolina. On 1 June, his ship repelled a Confederate cavalry attack at Secessionville. Three days later, he commanded Ellen during the attack on James Island.