The San Francisco Chronicle reports that the fire erupted around 10 a.m. Sunday on Mare Island near Vallejo.
Vallejo Fire Department Chief Paige Meyer said firefighters had tamed the blaze by 12:30 p.m. No one was injured.
Meyer says firefighters will monitor the smoldering ruin to make sure the fire does not re-ignite.
The 150,000-square-foot wooden structure at the defunct Mare Island Naval Shipyard was scheduled to be demolished sometime in the next year.
The Vallejo Fire Department says homeless people sometimes stayed in the warehouse and a campfire may have started the blaze, though no cause has been determined.