Admiral of the Fleet Sir Arthur Wilson VC, the Controller of the Royal Navy, summed up the opinion of many in the Admiralty at the time when he said in 1901 “Submarines are underhand, unfair, and damned un-English. Treat all submarines as pirates in wartime … and hang all crews.” In response, Lieutenant Commander (later Admiral) Max Horton first flew the Jolly Roger on return to port after sinking the German cruiser SMS Hela and the destroyer SMS S-116 in 1914 while in command of the E class submarine HM Submarine E9.

In World War II it became common practice for the submarines of the Royal Navy to fly the Jolly Roger on completion of a successful combat mission where some action had taken place, but as an indicator of bravado and stealth rather than of lawlessness. For example in 1982 returning from the Falklands conflict HM Submarine Conqueror flew the Jolly Roger depicting one dagger for the SBS deployment to South Georgia and one torpedo for her sinking of the Argentinean Cruiser Belgrano. (See Fig 1A-18a)

The Jolly Roger is the adopted emblem of the Royal Navy Submarine Service.