After various jobs in Kansas, Funston thirsted for adventure, and engaged in enterprises from Alaska to Central America before joining the Cuban Revolutionary Army fighting for independence from Spain in 1896.
Funston was in command in various engagements with Filipino nationalists. In April of 1899, he took a strongly defended Filipino position on the Rio Grande de la Pampanga at Calumpit. For his bravery, Funston was awarded the Congressional Medal of Honor and was soon after promoted to the rank of Brigadier General.
Funston played an important role in capturing Filipino leader Emilio Aguinaldo, on 23 March, 1901 at Palanan. When the capture of Aguinaldo was telegraphed back to the United States, Funston was widely hailed as a hero. Some considered Funston's reputation tarnished when details of the capture became known later on, as Funston's party gained access to Aguinaldo's camp by the ruse that the Americans were surrendering to the Filipinos.
In 1902 Funston toured the United States speaking to increase public support for the war in the Philippines. Mark Twain, a strong opponent of US Imperialism, published a sarcasm filled denunciation of Funston's mission and methods under the title "A Defence of General Funston" in the North American Review.
Funston was considered a useful advocate for US expansionism, but when he publicly made insulting remarks about anti-imperialist Republican Senator George Frisbie Hoar of Massachusetts, President Theodore Roosevelt thought Funston had gone too far and ordered a stop to his public speeches.
In 1906 Funston was in command of the Presidio base in San Francisco, California when the 1906 San Francisco Earthquake hit. Funston took command of the city under martial law, and directed the dynamiting of buildings to create fire-breaks to stop the out-of-control burning of the city. Funston's actions were later assessed with a mixture of criticism and praise. Some objected that he far exceeded his authority and acted contrary to military law, while others hailed him as a hero who did what was necessary in the face of the disaster.
From December 1907 through March of 1908 he was in charge of troops at the Goldfield mining center in Esmeralda County, Nevada, where the army to put down a labor strike by the Industrial Workers of the World.
General Funston was active in the conflict with Mexico in 1914 - 1916. He occupied the city of Veracruz, and later took part in the hunt for Pancho Villa. In November of 1914 he was made a Major General.
With the US entry into World War I, President Woodrow Wilson favored Funston to head up the American Expeditionary Force. Funston, however, died suddenly of a heart attack at the age of 51 years in San Antonio, Texas. The position of AEF commander went to General John J. Pershing.
Frederick Funston was buried in San Francisco. Shortly after his death, the Lake Merced military reservation (part of San Francisco's coastal defenses) was renamed Fort Funston in his honor.