Under her first commanding officer, Max Horton, J6 was launched on 9 September 1915 and commissioned on 25 January 1916. She and the other Js were members of the 11th Submarine Flotilla. She served in the North Sea chiefly in operations against German destroyers and U-boats. The closest she got to sinking the enemy was firing a torpedo at U-61, but it missed its target.
On 1 December 1917 Horton was replaced as commanding officer of J6 by Lieutenant Commander Geoffrey Warburton. In April 1918, Warburton spotted the German High Seas Fleet, which had put to sea in an attempt to hunt down an Allied convoy. Warburton did not identify the fleet as German and did not report his sighting to the Admiralty; had he done so, it is possible that another full scale naval battle may have occurred.[2]
On 15 October 1918 J6 was on patrol off the Northumberland coast when she was spotted by the Q-ship Cymric. The captain of the Cymric, Lieutenant F Peterson RNR, mistook the identity lettering on the conning tower of J6 for U6. Assuming U6 to indicate a German U-boat, Peterson raised the White ensign and opened fire on J6.[3] J6 tried to signal, but the signalman was killed. J6 fled into a fog bank, but Cymric located J6 again and sank her. After a number of direct hits, J6 sank. It was only after the survivors were seen in the water that Peterson and the crew of Cymric realised their mistake and recovered the survivors. Of the crew of J6, 15 were lost;[4] a subsequent court of enquiry found that no action would be taken against Peterson.[5] An order under the Official Secrets Act prohibited mention of this incident until 1969.[6]
Late in 2011 it was announced that divers had discovered her wreck off Seahouses.[7] In the summer of 2013, the Polish Navy salvage ship ORP Lech, searching for the wreck of the Polish submarine ORP Orzeł, surveyed and officially confirmed the identity of J6.[8]