Rooke joined the Board of Admiralty led by Admiral Edward Russell in May 1694. He also became commander-in-chief of the Mediterranean Fleet in August 1695 and then returned to England in April 1696. Promoted to Admiral of the Fleet shortly afterwards, he was given command the Channel Fleet but was unable to stop the French squadron which sailed from Toulon from reaching Brest and was criticised at the subsequent inquiry. He was elected Tory Member of Parliament for Portsmouth in Autumn 1698 and played an active part as spokesman for the Admiralty presenting, for example, an estimate of the navy debt to the House in April 1699. He was advanced to Senior Naval Lord on the Admiralty Board in May 1699.