In April 1902, Brigadier-General Funston was placed in command of the Department of the Colorado until March 1903, when he was placed in command of the Department of the Columbia. He was then placed in command of the Department of California.
Brigadier General Funston was the ranking officer at the Presidio in 1906 when one of the greatest natural disasters in California history, the San Francisco Earthquake, occurred on April 18, 1906. The shift in the San Andreas fault wrought havoc to the city, but the fires, fueled by debris and gas escaping from broken lines, sprang up in various sections of the city. Unfortunately, the quake also damaged water mains and to halt the spreading fires city officials decided to dynamite buildings to create fire lanes. The city fire chief sent an urgent request to the Presidio, an Army post on the edge of the stricken city, for dynamite.
At the time, Brigadier-General Funston, now commanding the Department of California and a resident of San Francisco had already decided the situation required the use of troops. He sent word to the Mayor offering assistance to civilian authorities.
During the first few days approximately 1,400 Army soldiers were ordered to the streets where they were joined by Navy sailors from nearby Mare Island Naval Shipyard, California Naval Militia and National Guardsmen in providing valuable services patrolling streets to discourage looting and guarding buildings such as the U.S. Mint, post office, and county jail. They aided the fire department in dynamiting to demolish buildings in the path of the fires.
The Army also became responsible for feeding, sheltering, and clothing the tens of thousands of displaced residents of the city. This support prompted many citizens to exclaim, "Thank God for the soldiers!"
Brigadier-General Frederick Funston, as the ranking officer at the Presidio, Funston assumed command of the city's military forces following the quake. Under the command of Major-General Adolphus Greely, Commanding Officer, Pacific Division, Funston's superior, who was in Washington, over 4,000 U.S. Army troops saw service during the emergency. There are conflicting reports as to whether he actually declared marshal law in order to contain looting and lawlessness. However, he offered troops and supplies to the city authorities and through this assistance much damage from fire and looting was prevented in the devastated area. On 1 July 1906 civil authorities assumed responsibility for relief efforts and the U.S. Army withdrew from the city. General Funston's actions were praised 11 years later by President Woodrow Wilson when he wrote: "His genius and manhood brought order out of confusion, confidence out of fear and much comfort in distress."
The general's next moment in the spotlight happened during the Mexican Border Conflict of 1914. The 49-year-old combat veteran had been sent to the area to take command of U.S. forces massing on the Texas border. This action was in response to the instability caused by the presidency of newly elected Mexican President Victoriano Huerta and the capture of several U.S. Marines. The city of Vera Cruz was ordered taken by President Wilson after a German merchant ship carrying munitions for Huerta was reported heading for the port. After a brief fight in which 17 Americans and 200 Mexicans were killed, Brigadier-General Funston was ordered to take 5,000 troops to the city to relieve the Navy and Marine personnel who had secured the city. He was then appointed military governor of the city.
Frederick Funston eventually earned the rank of major-general in 1916, making him the highest-ranking US Army officer.
The General was found again on the border of Mexico in 1916 following the slaying of unarmed Americans in Mexico and the raids of Francisco "Pancho" Villa north of the border had increased the tensions between the United States and Mexico. On March 9, 1916, Pancho Villa and 1,500 guerrillas attacked the New Mexico town of Columbus, killing 17 Americans. Funston recommended a pursuit of the outlaw, which was approved, however, his orders instructed him to send his subordinate, Brigadier-General John J. Pershing instead of going himself.
Instead Funston, supervised Pershing's "Punitive Expedition" from his headquarters in Texas, maintained security along the entire length of the Mexican border from the Gulf of Mexico to the California line. Although Pershing gained the headlines, Funston pioneered what was to become a future pattern of high level military command [and oversaw the federalization of 150,000 National Guardsmen]. In addition to General Pershing, Funston's subordinates during this time included future generals, then Captain Douglas MacArthur, Lieutenant George S. Patton, Jr., and Lieuteant Dwight D. Eisenhower.
On February 19, 1917, Major-General Funston was having dinner with friends at the St. Anthony Hotel in San Antonio, Texas, close to his headquarters at Fort Sam Houston. He had just finished dinner and was listening to the hotel orchestra play when a moment later he was dead. A heart attack took the life of the 51 year old major-general. The people of Texas showed their sincere respect by opening their most sacred shrine, the Alamo, so that he could lie in state there. He was the first person ever so honored. Ten thousand people paid their last respects to him during the three hours of public visitation. His body was then taken to the San Francisco City Hall Rotunda, where he laid in state for two days.
The nation had lost one of its greatest soldiers and California had lost one of its most celebrated heros. "Fearless Freddie," as the 5 foot 4 inch, 120-pound redhead was called after leading a charge through rifle fire during the Spanish-American War, who had endeared himself to the citizens of San Francisco by his policing of the city at the time of the 1906 earthquake and fire, was laid to rest at the Presidio (San Francisco National Cemetery) in full dress uniform on a hill overlooking the city he had saved.
Had he not died in early 1917 at the age of 52, evidence shows that President Woodrow Wilson would have picked him, not General John J. "Black Jack" Pershing, to command the American forces in World War I. But Funston died just months before the United States declared war, paving the way for General Pershing's ascension to high command.
Major-General Frederick Funston was a controversial figure, even in death. The Coast Artillery post on Rockaway Beach, New York, was originally named "Fort Funston" after General Frederick Funston. However, at the time of Funston's death in 1917, the name "Fort Funston" was already planned for the military reservation at Lake Merced, California. On June 26, 1917, the Lake Merced Military Reservation was named Fort Funston and on August 1, 1917, by order of General Order No.100 of the War Department, the name of the post in New York was officially changed to Fort Tilden in honor of Samuel Jones Tilden, a former Governor of New York, and the 1876 Democratic nominee for the Presidency of the United States.
Fort Funston, part of the U.S. coastal defense system for over 50 years, is now part of the Golden Gate National Recreation Area, named for General Frederick Funston, along with a street – "Funston Street" – at Fort Bragg.
Even after his death, the name Funston surfaced in another war – World War II. As a final tribute, the USS FREDERICK FUNSTON (APA-89) was launched on September 27, 1941, and was sponsored by Miss Barbara E. Funston. After serving with the Army Transportation Corps Fleet out of Seattle, the FREDERICK FUNSTON received six battle stars for her World War II service. She was turned to naval custody when the Military Sea Transportation Service was formed in 1950.