After returning home in late 1896, Lt. Vreeland was posted to the battleship USS Massachusetts in mid-January 1897, and served aboard her until he was transferred to the gunboat USS Helena at the end of June, whereupon he served through most of the Spanish-American War on blockade duty off the port of Manzanillo until the end of July 1898, even though he was named executive officer of the cruiser USS Dolphin in April of that year. He did not actually assume those duties until August 24. He was detached from the Dolphin to serve aboard the USS Olympia on November 6 that same year, but was ordered to the USS Concord instead on December 30 due to change in orders. Vreeland was promoted to lieutenant commander, and served aboard various vessels in the Asiatic Squadron. He returned home on board the hospital ship USS Solace in March 1900. From April 1900 to before August 1902 he was a member of the Board of Inspection and Survey, during which time he was promoted to full commander in mid-August 1901. After his duty in the Board, he supervised the fitting out of the new monitor USS Arkansas (later renamed the Ozark) and assumed command upon her commissioning on October 28 of that year.
Two years later, Vreeland relinquished command of the Ozark and served on shore a series of special assignments for the Department of the Navy for the next few years, during which he received his promotion to captain on April 13, 1906. After finishing his on-shore assignments in Washington, DC on April 17, 1907, Capt. Vreeland went to New York Ship in Camden, New Jersey the next day to commission the new Connecticut-class battleship USS Kansas. He commanded the battleship for the next two years, which was an auspicious time, for the Kansas was picked to be part of the "Great White Fleet" that sailed around the world. Soon after the Fleet returned to Hampton Roads on February 22, 1909 he gave up his command of the Kansas and returned home to await orders. On May 10, he succeeded Capt. Raymond P. Rodgers as Chief Intelligence Officer, the head of the Office of Naval Intelligence until December 8, when he was succeeded by Capt. Templin M. Potts.
On April 19, 1911 he reported ashore for further duty in Washington. In the newly devised aide system for managing the Navy, Vreeland became one of the four principal advisors of the Secretary of the Navy, George von Lengerke Meyer. As Aide for Inspections, he reached the pinnacle of naval command. During his tenure, he represented the Navy at the coronation of George V of the United Kingdom, as well as heading the so-called "Vreeland Board" which reinvestigated the sinking of the USS Maine in 1898, the controversial report of which — now widely regarded as erroneous — concluded that an external explosion sank the Maine.
On December 12, Rear Admiral Vreeland ended his tour of duty as Aide for Inspections and succeeded Rear Adm. Richard Wainwright as the second Aide for Operations. While in that position, Vreeland struggled to improve the defenses in the Philippine Islands, agitated for increased naval construction, particularly of battle cruisers, and supported the development of US naval aviation. It was also during his tenure that naval avaiation found a permanent home in Pensacola, Florida. On February 11, 1903 he was succeeded by Bradley A. Fiske as Aide for Operations, and Vreeland finished out his naval career as member of both the General and Joint Boards. He retired on March 10, 1914.
Rear Admiral Charles E. Vreeland died in Atlantic City, New Jersey after a brief retirement marked by illness.