She arrived at Key West on the 25th, the day on which President William McKinley signed a joint resolution of Congress that formalized the fact that a state of war had existed between the U.S. and Spain since the 21st.

On 8 May, she assisted Mayflower in capturing the Spanish sailing vessel Santiago Apostol, bound from Yucatan to Havana with a cargo of fish.

On 29 June, while she was on station at Guantánamo Bay with the torpedo boat Ericsson and cruiser Marblehead, Annapolis she assisted those ships in the capture of the British steamer Adula.

On 13 July, she left the Guantánamo Bay area to make a reconnaissance visit to Baracoa on Cuba's northeastern coast.

While at Baracoa on the 15th, she conferred with a group of friendly Cubans and engaged in a brief gun duel with an enemy shore battery near the eastern end of the town.

After a brisk exchange of fire, the Americans bested the Spanish warship in the resulting Battle of Nipe Bay, and she began to sink.

The gunboat departed Nipe Bay on 22 July and set a course for Puerto Rico where she assisted the Army in the capture of the city of Ponce on the 30th.

On 24 August, she departed Puerto Rico and proceeded—via Key West—to the New England coast where she visited Newport, Rhode Island; Portsmouth, New Hampshire; and New York City.

During that voyage, she visited Chefoo and Shanghai in China, Kobe and Yokohama in Japan and Tamsui on the island of Formosa before returning to Cavite on 19 November.

However, her stay was brief because she departed Cavite again on 2 June and shaped a course via Yokohama back to the U.S. Annapolis reached Mare Island, California, later that summer, was decommissioned, and entered the navy yard there for extensive repairs.

The warship made a stop at Honolulu on the way back, arrived at San Francisco on 9 October, and entered the Mare Island Navy Yard later that day.

At that time, she departed the Honduran coast and headed for Mexico where successive coups had unseated first Porfirio Díaz and then his successor Francisco Madero.

Gen. Victoriano Huerta seized the reins of government, but others—notably Venustiano Carranza, Emiliano Zapata, Álvaro Obregón, and Francisco "Pancho" Villa—contested his usurpation of power and generally added to the mayhem in Mexico.

[2] At 1915 on 21 September, while exercising off the Imperial fortress colony of Bermuda (where she was based at the Royal Naval Dockyard), the Royal Navy cruiser HMS Orion was ordered, in response to a request from the United States Consul for assistance, to make its way towards the position of Annapolis, four hundred miles from Bermuda at 35 degrees North and 54 degrees West.

On 30 June 1940, her name was struck from the Naval Vessel Register, and she was turned over to the United States Maritime Commission for disposal.