The newly completed HMS E5 sailed from Barrow in Furness for Portsmouth on 7 June 1913.  On 8 June 1913, whilst in the Irish Sea off Wales, E5 suffered an explosion in the Engine Room as the result of a diesel engine backfiring into the crankcase.  Three men died as a result of burns and injuries received.

In March 1916, HMS E5 (Lt Cdr H D Edwards) sailed for a patrol in the Heligoland Bight in company with HMS E23, E29, and H5. E5 failed to return. The last possible sighting of E5 was made by E29 during the afternoon of 6 March, 7 miles North of Juist Island in the North Sea. This was close to a German minefield, and it is possible that she struck a mine in this area. The exact reason for her loss, however, remains unknown.

In 2016, divers found the wreck of E5 off the island of Schiermonnikoog. Her hatches were open, which suggests that the crew may have tried to escape. There was no obvious sign of damage to her hull, indicating that she had perhaps not sunk as a result of enemy action.