After training in Chesapeake Bay, Whipple was assigned to the 2d Torpedo Flotilla, Atlantic Fleet, and was based at Norfolk. The destroyer periodically served as flagship of the flotilla and operated off the east coast and in the Caribbean until she was placed in reserve at Norfolk on 5 September 1905.
Returning to active service on 16 July 1906, the ship conducted tactical exercises and routine training operations through November of 1907. On 2 December, Whipple stood out of Hampton Roads and headed south toward the Caribbean for goodwill visits—“showing the flag.”
Subsequently following in the wake of the 16 battleships of the Great White Fleet, Whipple and her flotilla-mates called at Rio de Janeiro; rounded Cape Horn for ports on the Chilean and Peruvian coasts; and conducted target practice at Magdalena Bay, Mexico. After participating in a fleet review at San Francisco on 8 May 1908, Whipple remained on the West Coast, based at San Diego as a unit of the Pacific Torpedo Flotilla.
Departing San Francisco at the end of a towline on 24 August, the destroyer subsequently took part in fleet battle problems in Hawaiian waters. Upon completion of the exercises, she steamed back to the West Coast via Samoa and Magdalena Bay, Baja California, arriving at San Diego on 1 December.
For the next six years, Whipple operated off the West Coast between San Diego and Magdalena Bay and made one cruise to Alaskan waters for maneuvers. She received the Mexican Service Medal for service off the Mexican coast in 1914 and 1916. While that country suffered in the throes of revolution and civil strife, the destroyer conducted patrols and stood ready to protect American lives and property.
On 6 April 1917, America entered World War I on the side of Britain, France, and Italy. Whipple soon commenced patrols off the approaches to the vital Panama Canal before departing the Canal Zone on 5 July.
Refitted for “distant service,” the destroyer put to sea on 28 August, bound for the Atlantic war zone, and put into the Azores on 17 September. Whipple operated on escort duties, convoying ships to and from the strategic islands for the next three months. She then received orders to report at Brest, France.
Antisubmarine patrols and convoy escort duties occupied Whipple through the early spring of 1918. On 17 April, munitions ship Florence H. blew up off Quiberon Bay. Braving flying debris from the exploding ship, Whipple joined Stewart (Coast Torpedo Vessel No. 13) and Truxtun (Coast Torpedo Vessel No. 14) in rescuing 32 men of the 77-man crew of that doomed vessel.
Whipple carried out her routine wartime patrol duties through the end of hostilities. On 9 December, she departed the French coast and headed homeward, touching at the Azores and Bermuda before making port at Philadelphia on 3 January 1919.
Whipple was decommissioned at the Philadelphia Navy Yard on 7 July 1919 and her name was struck from the Navy list on 15 September. On 3 January 1920, J. G. Hitner of Philadelphia purchased her for scrapping.