Flag was purchased on 26 April 1861 as Phineas Sprague, and renamed and commissioned on 28 May 1861, Lieutenant Commander L. C. Sartori in command.
Flag reported for duty in the South Atlantic Blockading Squadron at Charleston, South Carolina on 6 June 1861. Aside from periods in the North for repairs, she patrolled the coastal waters of the Carolinas until early 1865. Flag captured or shared in the capture of many blockade runners.
On 24 November, she joined Seneca and Pocahontas in taking possession of Tybee Island, evacuated previously by the Confederates, and two days later drove several southern ships back into Fort Pulaski, from which they were attempting to sail. She participated in the capture of Fernandina, Florida in March 1862, and in the general engagement of the fleet with the forts in Charleston Harbor on 7 April 1863.
She returned to New York on 16 February 1865, was decommissioned there on 25 February, and sold on 12 July.
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