"New York" was transferred to the Asiatic Fleet in 1901, sailing via Gibraltar, Port Said, and Singapore to Cavite, where she became flagship of the Asiatic Fleet. She steamed to Yokohama in July for the unveiling of the memorial to the Perry Expedition. In October, "New York" visited Samar and other Philippine islands as part of the campaign against insurgents. On 13 March 1902, she got underway for Hong Kong and other Chinese ports. In September, she visited Vladivostok, Russia, then stopped at Korea before returning to San Francisco in November. In 1903, "New York" transferred to the Pacific Squadron and cruised with it to Ampala, Honduras in February to protect American interests during turbulence there. Steaming via Magdalena Bay, Mexico, the cruiser returned to San Francisco, for a reception for President Theodore Roosevelt. In 1904, "New York" joined squadron cruises off Panama and Peru, then reported to Puget Sound in June where she became flagship of the Pacific Squadron. In September, she enforced the President's neutrality order during the Russo-Japanese War. "New York" was at Valparaíso, Chile from 21 December 1904 – 4 January 1905, then sailed to Boston and decommissioned on 31 March for modernization.