Construction of the Fort Worden military defense installation began in 1896. It was one of three major fortifications protecting Puget Sound. The three, Fort Casey, Fort Flagler, and Fort Worden eventually became known as the triangle of fire, protecting the Puget Sound entrance from feared Spanish American War naval attacks, and any naval attacks from other nations.
Fort Worden was activated in May 1902 and was named for a naval officer, Admiral John Lorimer Worden (1818–1897), captain of the ironclad Civil War vessel USS Monitor.
The first troops arrived in May 1902 and Fort Worden was fully operational in 1905 as the Headquarters of the Puget Sound Harbor Defense Command. On June 2, 1902, one month after post activation, the first death occurred. Private Elisha Webb (1879–1902) of McMinn County, Tennessee died of illness. Private Webb was a soldier in the 126th Coast Artillery and he was buried in the new cemetery.
In 1903 the Secretary of War directed that Fort Worden be the official burial grounds for the three Puget Sound harbor defense forts. Since then, the cemetery has over 430 interments that include service members, spouses and dependents from the Spanish American War to current engagements.
In 1908, a monument named the Soldiers' Monument was erected in the cemetery. It had a pivot gun off the revenue cutter Jefferson Davis placed on a concrete pedestal. The monument honors all those who died in the service of this nation. During a scrap metal drive for World War II the pivot gun was removed and melted down for the war effort. It was replaced with a 1918 German howitzer. The gun and pedestal, along with the American Flag, are the center features of the cemetery.
In World War I artillery Soldiers going to European battlefields trained here. Between the wars the post had a small force and rearmed. In World War II the Fort was home to the 14th Coast Artillery Regiment and the joint Navy-Army Harbor Defense Command. Emphasis shifted to anti-aircraft artillery. Outdated coastal artillery was scrapped.
After World War II, Fort Worden was determined to be obsolete and the Harbor Defense Command closed in June 1953. In 1957 Washington State purchased the property for a youth treatment center. Budget cuts in 1971 closed the youth treatment center and it then became a Washington state park. The cemetery was not included in the land transfer and remained an active Army cemetery until transferred to the National Cemetery Administration in August 2020.