After fitting out as an auxiliary cruiser, the ship joined in the Spanish–American War and patrolled the coastal waters between Block Island and Cape Henlopen until 27 May.

While St. Louis dragged for and cut the three cables, Yankee and Marblehead covered her activities by engaging the Spanish gunboats Alvarado and Sandoval.

After putting the Spanish gunboats to flight, the two American warships turned their attention toward the fort at Caimanera which had been making a nuisance of itself with its single large-caliber gun—a venerable, smooth-bore muzzleloader.

At about noon on 10 June, Yankee set a course for Port Antonio, Jamaica, to deliver dispatches and to search for the suspected blockade runner SS Purissima Concepcion.

However, that same day, she received orders to move again, this time to Cienfuegos, about halfway up the southern coast of Cuba from Santiago, to stand guard there against Purissima Concepcion's expected run.

Yankee cleared for action and stood in toward the warship, but all hands breathed a sigh of relief when the newcomer was identified as the neutral German SMS Geier.

The following afternoon, the auxiliary cruiser gave up her vigil for Purissima Concepcion off Cienfuegos and set a course back to the eastern end of Cuba.

At about 08:30 on the morning of 20 June, Yankee sighted a steamer lying in Casilda harbor closely fitting the description of Purissima Concepcion.

The American ship stood in as close to the shoals as she dared and then fired a shot across the steamer's bow in an unsuccessful effort to make her show her colors.

The extreme range—in excess of 5,000 yd (4,600 m)—made the gunfire from both sides so ineffective that Yankee broke off the engagement and resumed her patrols between Casilda and Cienfuegos.

The auxiliary cruiser continued her blockade of that stretch of the Cuban coast until 24 June, when her dwindling supply of coal forced her to head for Key West.

En route to that base, she visited the Isle of Pines where she captured and destroyed five Spanish fishing vessels on 25 June.

Three days later, while she cruised the northern coast of Cuba, Yankee received word of the cessation of hostilities in response to Spain's suit for peace.

Early in December 1903, she headed south for winter maneuvers and gunnery drills with the North Atlantic Fleet in the gulf and the Caribbean around Hispaniola.

After visiting a number of West Indian ports in conjunction with the exercises, she returned north late in March 1904, and on 6 April, was moored to a pier at League Island where she remained until October.

After a return voyage to Newport News, she headed for League Island where she entered the navy yard for repairs on 13 January.

Successive coups since assassination of the dictator Heureaux in 1899 had added civil strife and anarchy to the list of woes of a country already racked by desperate financial problems.

[3] The ship, by then classified as a transport, left for Santo Domingo on 21 August 1906 and after participating in the Presidential Naval Review held at Oyster Bay from 2 to 4 September, she unloaded stores at New York in preparation for inactivation.