USS Neptune has been the name of more than one United States Navy ship, and may refer to:

• USS Clyde (1863)
  USS Clyde (1863)
  USS Clyde was a steamer captured by the Union Navy during the American Civil War. She was assigned by the Union Navy to patrol navigable waterways of the Confederacy to prevent the South from trading with other countries....
  
  , a 294-ton side-wheel steam gunboat, was briefly named Neptune when first commissioned

, a 1244-ton screw steamship, served during the American Civil War
, a monitor in commission from 1864 to 1877, briefly named USS Neptune during 1869

• USS Neptune (AC-8)
  USS Neptune (AC-8)
  The third USS Neptune , a collier of the U.S. Navy, was laid down by the Maryland Steel Co., Sparrows Point, Md. 23 March 1910; launched 21 January 1911; and placed in service with a merchant crew at Norfolk Navy Yard 20 September 1911, Master F. E...
  
  , was a collier that carried the first United States troops to Europe in World War I

, was a Neptune-class cable repair ship, acquired by the US Navy in 1953 and scrapped in 2005

In fiction

• A fictitious U.S. Navy nuclear submarine named USS Neptune was the setting of the 1978 movie Gray Lady Down
  Gray Lady Down
  Gray Lady Down is a 1978 disaster film by Universal Studios starring Charlton Heston, David Carradine, Stacy Keach, Ned Beatty, Ronny Cox, and features the first film role for a young Christopher Reeve...