At the start of hostilities the Orzel was on patrol in it's designated sector of the Baltic. Unable to return to the Polish Naval Base at Gdynia or Hel, Orzel had to make it's way into a neutral port to offload it's sick captain. The crew chose to go to Tallinn, Estonia. In danger of being interned, the crew elected to escape with ship and make the perilous journey to England. Under the new command of the it's former XO, Lt.Cdr. Jan Grudzinski, the Orzel escaped, evaded the numerous Kriegsmarine ships hunting for her, and made it to England.
After refitting and rest, the Orzel went immediately on patrol. It sank the German Troop Transport "Rio de Janeiro" that was heading for the invasion of Norway in early May 1940.
The Orzel was lost with all hands on the next patrol somewhere in the North Sea, in late May 1940.