At 01.16 hours on 14 October 1939 U-47 fired a spread of three torpedoes at HMS Royal Oak (08) (Capt W.G. Benn, RN) and the British seaplane tender HMS Pegasus lying at anchor in the harbour of Scapa Flow, then turned around and fired a stern torpedo at 01.21 hours. Prien claimed a hit on the seaplane tender, misidentified as HMS Repulse (34), but one of the torpedoes apparently hit the starboard anchor chain of the battleship and both targets were undamaged.

At 01.23 hours, the U-boat fired a second spread of three torpedoes which hit HMS Royal Oak (08) on the starboard side and caused a magazine to blow up. The battleship rolled over and sank in 19 minutes. 386 of the survivors, including the commander, were rescued by the drifter HMS Daisy II (Skipper John Gatt) which had been alongside as tender.