HMS J6 was commissioned on 25 January 1916 by Commander Max Horton DSO, who was appointed to supervise her building and remained in command for 18-months.

HMS J6 (Lt Cdr G Warburton) was attacked in error by the Q ship HMS CYMRIC off Blyth on 15 October 1918. CYMRIC fired three rounds and all three hit J6.

Because there were few J class submarines in service, the Q ship crew were not familiar with the class and mistook her for a German U-boat. Their recognition was further confused by what they took to be a sign painted on the side of the fin, U6 . In fact, this was J6 slightly obscured by an object hanging over the side of the bridge.

The shells from HMS CYMRIC killed the lookout on the bridge who was trying to signal to CYMRIC, and a second shell hit the control room. J6 disappeared into a fog bank and CYMRIC followed. She was sighted again, sinking in flat calm conditions. Some of her crew were trying to escape in a small collapsible boat. At this point CYMRIC realised that she was attacking a Royal Navy submarine and promptly attempted to rescue as many of the ship company as possible but only about 15 survived.

At the subsequent Board of Inquiry, CYMRIC was absolved of blame. CYMRIC commanding officer had been decorated with two DSOs and two DSCs for previous bravery; when he left the room in which the inquiry was being held, those survivors from J6 present stood smartly to attention and saluted.

Late in 2011 it was announced that divers had discovered her wreck off Seahouses, Northumberland. In the Summer of 2013, the Polish Navy salvage ship ORP Lech, searching for the wreck of the Polish submarine ORP ORZEL, surveyed and officially confirmed the identity of J6.