After 18 months of inactivity, the gunboat was re-commissioned at Boston on 15 August 1900, Comdr. Francis H. Delano in command. She departed Boston on 19 September and, after a five-day stop at Tompkinsville, New York, embarked upon a training cruise to the Mediterranean on 27 September. Steaming via the Azores and Lisbon, Portugal, and Gibraltar, she entered the Mediterranean on 7 November. During the cruise, she visited Villefranche, Genoa, Livorno, Naples, Algiers, and Tangier. "Topeka", transited the Strait of Gibraltar on 5 January 1901 and, after visits to the Azores and to St. Vincent and Barbados in the West Indies, returned to the United States at Hampton Roads, Virginia, on 4 March 1901.