He served during the War of the Spanish Succession and is known for his role in the Capture of Gibraltar and the Battle of Málaga in 1704.
He joined the Royal Navy and he was promoted to a lieutenant of HMS Swallow on 16 October 1688 under Matthew Aylmer.
For three years he and his crew captured many French privateers and supporting prize money.
[1] In 1693 he returned to support Aylmer who was now an admiral and he was his flag-captain in HMS Royal Sovereign.
On 13 January 1702 fifty ships were commissioned on one day and Whitaker briefly was given HMS Ranelagh before he became master-attendant at Woolwich.
In 1705 Whitaker commanded HMS Barfleur and in the first few months of 1706 he became Sir Edward Whitaker, rear-admiral of the blue, commanding a squadron of ships in the English Channel escorting the Duke of Marlborough to Holland in April.