Capt. Wesley Aaron Smith, 50, was alone when rescue crews found him unresponsive about 8 p.m., according to Navy Region Southeast public affairs.
The cause of death has not been determined as the fire remains under investigation, and no more information is expected until Tuesday at the earliest, said Navy Region Southeast spokesman Steve Strickland.
"Our heart goes out to the family," he said.
Rear Adm. Brian Luther, who commands Carrier Strike Force Group Two, offered his condolences to the captain's family and the crew of almost 400 on board the guided-missile cruiser.
"They are in our thoughts and prayers as we deal with this tragic loss," he said. "Capt. Smith served the Navy and our nation honorably and with great distinction."
Smith had been in command of the Philippine Sea for almost exactly two years when he died.
A surface warfare officer, he was originally from Virginia and had been in the Navy since 1990. Prior to commanding the Philippine Sea, he was captain of the USS The Sullivans. He assumed command of the Philippine Sea on Oct. 4, 2013, taking over for Capt. Steve Shinego. At the time, Smith told the Mayport Mirror that it is "a great opportunity to serve on a great ship."
Smith is survived by his wife and two children. Funeral arrangements are still being made, according to the Navy.
Temporary command of the Philippine Sea has been given to Cmdr. Nathan Rowan as the ship remains docked at Mayport.