After completion in September 1940, HMS Phoebe (43) (Capt G. Grantham, RN) was assigned the 15th Cruiser squadron as part of the Home Fleet and used in the North Atlantic on trade protection duties. In April 1941, she joined the Mediterranean fleet at Alexandria from where she took part in the evacuation of Greece and Crete and some Malta convoys. She returned to Alexandria on 29 May with New Zealand troops evacuated from Crete, but was sent back to Crete accompanied by the destroyers HMAS Napier (G 97), HMAS Nizam (G 38), HMS Kelvin (F 37) and HMS Kandahar (F 28) to evacuate as many as possible of the remaining New Zealand and Australian soldiers before Crete capitulated. The cruiser served then as flagship in the operations against the Vichy-French Syria in June.

At 20.05 hours on 3 Jul 1941, the Italian submarine Malachite (Zanni) fired torpedoes at HMS Phoebe (43) in 32°25N/24°40E and heard a detonation after two minutes and claimed the sinking of the cruiser, which was in fact missed. On 27 Aug 1941, HMS Phoebe (43) was hit by a torpedo from an Italian aircraft while covering troop transports to the besieged Tobruk. Temporary repairs were made at Alexandria and the cruiser then left to New York for permanent repairs, which were made between 21 November and 21 Apr 1942 and she returned to service in May 1942. After the transfer to the Mediterranean, the cruiser took part in Operation Pedestal in August 1942 as escort for the aircraft carriers that brought Spitfires to Malta. The following month, she and HMS Sirius (82) were stationed in Capetown to patrol against Axis blockade runners, but had no success.

After returning to service in July 1943, HMS Phoebe (43) returned to the Mediterranean again and operated first in the Aegean and then took part in Operation Shingle, the landings at Anzio in January 1944. Later that year she joined the 5th Cruiser Squadron as part of the Eastern Fleet and operated in the Indian Ocean until war´s end. The cruiser covered the carrier raids on the Nicobars and Sabang as a fighter direction ship and the assault landings on the coast of Burma and the Rangoon landings in April/May 1945. During this time she was flagship of the 21st Escort Carrier Squadron, until relieved by HMS Royalist (89).

On 29 Oct 1945, the cruiser arrived at Sheerness to refit and in 1946 joined the Mediterranean Fleet as flagship for the Destroyer Flotillas until November 1947, when she was assigned to the the 1st Cruiser Squadron. On 14 Mar 1951, the ship arrived at Chatham to be paid off, then acted as senior officer´s ship in the Harwich reserve until 1955, followed by a year with the Portsmouth reserve. On 1 Aug 1956, the ship arrived at Hughes Bolkow, Blyth to be broken up.

At 07.56 hours on 23 Oct 1942, HMS Phoebe (43) (Capt C.P. Frend, RN) was hit on the port side forward and aft by two torpedoes from U-161 six miles 282° from Pointe Noire, French Equatorial Africa. The U-boat reported the torpedoeing of a Balch class destroyer and observed the lowering of boats but was then chased away by a corvette. The badly damaged cruiser continued at 6 knots to Point Noire and was beached there.

After temporary repairs and removal of the first turret left in December via Takoradi and Trinidad to New York, escorted by HMS Bridgewater (L 01) (Cdr N.W.H. Weekes, OBE, Rtd, RN). Permanent repairs lasted from January to June 1943 the cruiser then went to the Vickers Armstrong Shipyard at Barrow in Furness to be fitted with a new turret and returned to service in August.