Capture of U-505

Returning to New York 27 April 1944, Flaherty rejoined the Guadalcanal group at Norfolk, Virginia, 10 May, and 5 days later sailed on a patrol which was to win the task group a Presidential Unit Citation. On 4 June, in a well-planned and executed operation, her group captured intact German submarine U-505. The only capture by American forces of a German submarine on the high seas during the war, this dramatic operation provided essential intelligence for future antisubmarine warfare. Flaherty's role during the action was close screening for Guadalcanal, from which the attack and seizure were directed. She returned to New York from this patrol 22 June.

Sinking of U-546

Between 15 July 1944 and 7 November, Flaherty completed two more hunter-killer patrols with the Guadalcanal group, then served as school ship for the Naval Training Center at Miami, Florida. Training in the Caribbean with carriers followed, until she sailed from Naval Station Mayport, 9 April for Argentia, Newfoundland. This was her base for duty on the barrier line established in the last months of the European phase of the war to prevent desperate U-boats from penetrating the western Atlantic. On 24 April, USS Frederick C. Davis was torpedoed while investigating a submarine contact, and Flaherty dashed to rescue her survivors. After three men had been taken on board, Flaherty picked the submarine up by sonar, and moved in to attack. Seven other escorts joined her in the 10-hour hunt, which resulted in forcing German submarine U-546 to the surface, where she was sunk by gunfire. She recovered five of the U-boat's survivors, including the commanding officer.

Flaherty returned to New York 11 May 1945, and 2 weeks later sailed on convoy escort duty to Le Havre, France, and Southampton, England. She returned to duty guarding carriers training off Norfolk and Charleston, South Carolina, until arriving at Green Cove Springs, Florida, 12 January 1946.