After service with Edward Preble's squadron in the Mediterranean and a cruise to the East Indies, Henley received his first command, Gunboat No.

5, at Baltimore, Maryland on 9 April 1808. Henley was in command of two divisions of 15 gunboats which drove three British frigates from Hampton Roads on 20 June 1813.

Reporting to brig Eagle, he received the Thanks of Congress and a Congressional Gold Medal for valiant conduct in the Battle of Lake Champlain 11 September 1814.

With the end of the War of 1812, Henley filled a variety of billets before commanding Hornet against pirates in the West Indies.

After serving as commandant of the Naval Rendezvous at Norfolk 1822 to 1824, he reported for similar duty at Charleston, South Carolina.