"Yankee" stopped briefly at Tompkinsville at the end of August and then made a round-trip voyage to League Island, and back to Tompkinsville at the beginning of September. She returned to League Island on 19 September. There, her crew of New York Naval Militia reservists left the ship to return home via train for mustering out. Though she remained in commission technically until decommissioned on 16 March 1899, "Yankee" spent the interim at League Island. That location also remained her home for the more than three years she spent in reserve. Her inactivity ended when she was placed back in commission on 1 May 1903, Commander G. P. Colvocoressee in command.